metadata: run_metadata: 642 rows where devstage_curation = "Adult" and experiment.library

642 rows where devstage_curation = "Adult" and experiment.library_selection = "PolyA"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	sample.description	sample.title	sample.alias	sample.centername	sample.attributes	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.spot_descriptor	experiment.study_ref	run.title	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.r3_length	run.r4_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.mapping_rate.mate2	seqdetective.nofeature_rate.mate1	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.pos_strand_rate.mate2	seqdetective.readlen.mate1	seqdetective.readlen.mate2	seqdetective.judgement.mate1	seqdetective.judgement.mate2	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
23	23	DRR334968	DRX323964	DRS217304	DRP008001	PRJDB12578	Allometric scaling of RNA abundance from genes to communities	DRP008001	Other	The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole body RNA content in organisms. However testing RNA allometric scaling with next generation sequencing is yet to be done. Here we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling while the assumed temperature dependence appeared to be weak. Lastly allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes.		mRNA metatranscriptomic sequences from mock communities consist of five model species	mRNA mock community at 28 degrees rep 3	SAMD00422588		sample name:mRNA mock community 28 degrees rep 3\|biological replicate:3\|collection date:2021 01 15\|dev stage:Adult\|technical replicate:3\|temp:28\|treatment:mRNA	NextSeq 2000 sequencing of SAMD00422588	DRX323964	m28 3 mRNA.fastq	1	NEBNext Kit for Illumina		RNA-Seq	METATRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP008001	NextSeq 2000 sequencing of SAMD00422588				3157078356.0	31416275.0	DRR334968	0:100.49 1:0	A:816263259;C:752748024;G:759884392;T:828182261;N:420	100	0			816263259	752748024	759884392	828182261	420	DRX323964	DRS217304	DRA013226	SINICA\|Machida Laboratory Biodiversity Research Center, Academia Sinica	SINICA\|Machida Laboratory Biodiversity Research Center, Academia Sinica	1	0.64888		0.01832		0.73996		0.46811		99		B		usable mapping rate	illumina	nextseq_v2	unknown	poly_a	nebnext	bulk	unknown	unknown	Taiwan	2021-12-23	Adult	Adult	Undetermined	Undetermined
24	24	DRR334967	DRX323963	DRS217303	DRP008001	PRJDB12578	Allometric scaling of RNA abundance from genes to communities	DRP008001	Other	The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole body RNA content in organisms. However testing RNA allometric scaling with next generation sequencing is yet to be done. Here we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling while the assumed temperature dependence appeared to be weak. Lastly allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes.		mRNA metatranscriptomic sequences from mock communities consist of five model species	mRNA mock community at 28 degrees rep 2	SAMD00422587		sample name:mRNA mock community 28 degrees rep 2\|biological replicate:3\|collection date:2021 01 15\|dev stage:Adult\|technical replicate:2\|temp:28\|treatment:mRNA	NextSeq 2000 sequencing of SAMD00422587	DRX323963	m28 2 mRNA.fastq	1	NEBNext Kit for Illumina		RNA-Seq	METATRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP008001	NextSeq 2000 sequencing of SAMD00422587				3155807651.0	31404635.0	DRR334967	0:100.49 1:0	A:819014350;C:749873295;G:756284406;T:830635394;N:206	100	0			819014350	749873295	756284406	830635394	206	DRX323963	DRS217303	DRA013226	SINICA\|Machida Laboratory Biodiversity Research Center, Academia Sinica	SINICA\|Machida Laboratory Biodiversity Research Center, Academia Sinica	1	0.76742		0.02238		0.72427		0.47376		101		B		usable mapping rate	illumina	nextseq_v2	unknown	poly_a	nebnext	bulk	unknown	unknown	Taiwan	2021-12-23	Adult	Adult	Undetermined	Undetermined
25	25	DRR334966	DRX323962	DRS217302	DRP008001	PRJDB12578	Allometric scaling of RNA abundance from genes to communities	DRP008001	Other	The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole body RNA content in organisms. However testing RNA allometric scaling with next generation sequencing is yet to be done. Here we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling while the assumed temperature dependence appeared to be weak. Lastly allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes.		mRNA metatranscriptomic sequences from mock communities consist of five model species	mRNA mock community at 28 degrees rep 1	SAMD00422586		sample name:mRNA mock community 28 degrees rep 1\|biological replicate:3\|collection date:2021 01 15\|dev stage:Adult\|technical replicate:1\|temp:28\|treatment:mRNA	NextSeq 2000 sequencing of SAMD00422586	DRX323962	m28 1 mRNA.fastq	1	NEBNext Kit for Illumina		RNA-Seq	METATRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP008001	NextSeq 2000 sequencing of SAMD00422586				2589772286.0	25765782.0	DRR334966	0:100.51 1:0	A:679223577;C:610675892;G:617869465;T:682003195;N:157	100	0			679223577	610675892	617869465	682003195	157	DRX323962	DRS217302	DRA013226	SINICA\|Machida Laboratory Biodiversity Research Center, Academia Sinica	SINICA\|Machida Laboratory Biodiversity Research Center, Academia Sinica	1	0.42984		0.03367		0.73555		0.49223		100		B		usable mapping rate	illumina	nextseq_v2	unknown	poly_a	nebnext	bulk	unknown	unknown	Taiwan	2021-12-23	Adult	Adult	Undetermined	Undetermined
26	26	DRR334965	DRX323961	DRS217318	DRP008001	PRJDB12578	Allometric scaling of RNA abundance from genes to communities	DRP008001	Other	The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole body RNA content in organisms. However testing RNA allometric scaling with next generation sequencing is yet to be done. Here we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling while the assumed temperature dependence appeared to be weak. Lastly allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes.		mRNA metatranscriptomic sequences from mock communities consist of five model species	mRNA mock community at 19 degrees rep 3	SAMD00422602		sample name:mRNA mock community 19 degrees rep 3\|biological replicate:2\|collection date:2021 01 15\|dev stage:Adult\|technical replicate:3\|temp:19\|treatment:mRNA	NextSeq 2000 sequencing of SAMD00422602	DRX323961	m19 3 mRNA.fastq	1	NEBNext Kit for Illumina		RNA-Seq	METATRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP008001	NextSeq 2000 sequencing of SAMD00422602				3124746628.0	31095367.0	DRR334965	0:100.49 1:0	A:821891547;C:734660854;G:739230475;T:828963220;N:532	100	0			821891547	734660854	739230475	828963220	532	DRX323961	DRS217318	DRA013226	SINICA\|Machida Laboratory Biodiversity Research Center, Academia Sinica	SINICA\|Machida Laboratory Biodiversity Research Center, Academia Sinica	1	0.72881		0.03264		0.69449		0.47416		99		B		usable mapping rate	illumina	nextseq_v2	unknown	poly_a	nebnext	bulk	unknown	unknown	Taiwan	2021-12-23	Adult	Adult	Undetermined	Undetermined
27	27	DRR334964	DRX323960	DRS217317	DRP008001	PRJDB12578	Allometric scaling of RNA abundance from genes to communities	DRP008001	Other	The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole body RNA content in organisms. However testing RNA allometric scaling with next generation sequencing is yet to be done. Here we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling while the assumed temperature dependence appeared to be weak. Lastly allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes.		mRNA metatranscriptomic sequences from mock communities consist of five model species	mRNA mock community at 19 degrees rep 2	SAMD00422601		sample name:mRNA mock community 19 degrees rep 2\|biological replicate:2\|collection date:2021 01 15\|dev stage:Adult\|technical replicate:2\|temp:19\|treatment:mRNA	NextSeq 2000 sequencing of SAMD00422601	DRX323960	m19 2 mRNA.fastq	1	NEBNext Kit for Illumina		RNA-Seq	METATRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP008001	NextSeq 2000 sequencing of SAMD00422601				3171661466.0	31561473.0	DRR334964	0:100.49 1:0	A:836793307;C:742872021;G:750053514;T:841942389;N:235	100	0			836793307	742872021	750053514	841942389	235	DRX323960	DRS217317	DRA013226	SINICA\|Machida Laboratory Biodiversity Research Center, Academia Sinica	SINICA\|Machida Laboratory Biodiversity Research Center, Academia Sinica	1	0.63153		0.03639		0.69027		0.48494		101		B		usable mapping rate	illumina	nextseq_v2	unknown	poly_a	nebnext	bulk	unknown	unknown	Taiwan	2021-12-23	Adult	Adult	Undetermined	Undetermined
28	28	DRR334963	DRX323959	DRS217316	DRP008001	PRJDB12578	Allometric scaling of RNA abundance from genes to communities	DRP008001	Other	The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole body RNA content in organisms. However testing RNA allometric scaling with next generation sequencing is yet to be done. Here we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling while the assumed temperature dependence appeared to be weak. Lastly allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes.		mRNA metatranscriptomic sequences from mock communities consist of five model species	mRNA mock community at 19 degrees rep 1	SAMD00422600		sample name:mRNA mock community 19 degrees rep 1\|biological replicate:2\|collection date:2021 01 15\|dev stage:Adult\|technical replicate:1\|temp:19\|treatment:mRNA	NextSeq 2000 sequencing of SAMD00422600	DRX323959	m19 1 mRNA.fastq	1	NEBNext Kit for Illumina		RNA-Seq	METATRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP008001	NextSeq 2000 sequencing of SAMD00422600				2916453082.0	29023768.0	DRR334963	0:100.48 1:0	A:761416880;C:692014182;G:696272089;T:766749729;N:202	100	0			761416880	692014182	696272089	766749729	202	DRX323959	DRS217316	DRA013226	SINICA\|Machida Laboratory Biodiversity Research Center, Academia Sinica	SINICA\|Machida Laboratory Biodiversity Research Center, Academia Sinica	1	0.71651		0.03406		0.68696		0.47496		101		B		usable mapping rate	illumina	nextseq_v2	unknown	poly_a	nebnext	bulk	unknown	unknown	Taiwan	2021-12-23	Adult	Adult	Undetermined	Undetermined
29	29	DRR334962	DRX323958	DRS217315	DRP008001	PRJDB12578	Allometric scaling of RNA abundance from genes to communities	DRP008001	Other	The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole body RNA content in organisms. However testing RNA allometric scaling with next generation sequencing is yet to be done. Here we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling while the assumed temperature dependence appeared to be weak. Lastly allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes.		mRNA metatranscriptomic sequences from mock communities consist of five model species	mRNA mock community at 10 degrees rep 3	SAMD00422599		sample name:mRNA mock community 10 degrees rep 3\|biological replicate:1\|collection date:2021 01 15\|dev stage:Adult\|technical replicate:3\|temp:10\|treatment:mRNA	NextSeq 2000 sequencing of SAMD00422599	DRX323958	m10 3 mRNA.fastq	1	NEBNext Kit for Illumina		RNA-Seq	METATRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP008001	NextSeq 2000 sequencing of SAMD00422599				2600103192.0	25872833.0	DRR334962	0:100.50 1:0	A:668944597;C:625686885;G:631010166;T:674461210;N:334	100	0			668944597	625686885	631010166	674461210	334	DRX323958	DRS217315	DRA013226	SINICA\|Machida Laboratory Biodiversity Research Center, Academia Sinica	SINICA\|Machida Laboratory Biodiversity Research Center, Academia Sinica	1	0.57077		0.02949		0.71918		0.47633		101		B		usable mapping rate	illumina	nextseq_v2	unknown	poly_a	nebnext	bulk	unknown	unknown	Taiwan	2021-12-23	Adult	Adult	Undetermined	Undetermined
30	30	DRR334961	DRX323957	DRS217314	DRP008001	PRJDB12578	Allometric scaling of RNA abundance from genes to communities	DRP008001	Other	The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole body RNA content in organisms. However testing RNA allometric scaling with next generation sequencing is yet to be done. Here we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling while the assumed temperature dependence appeared to be weak. Lastly allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes.		mRNA metatranscriptomic sequences from mock communities consist of five model species	mRNA mock community at 10 degrees rep 2	SAMD00422598		sample name:mRNA mock community 10 degrees rep 2\|biological replicate:1\|collection date:2021 01 15\|dev stage:Adult\|technical replicate:2\|temp:10\|treatment:mRNA	NextSeq 2000 sequencing of SAMD00422598	DRX323957	m10 2 mRNA.fastq	1	NEBNext Kit for Illumina		RNA-Seq	METATRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP008001	NextSeq 2000 sequencing of SAMD00422598				2608660833.0	25958804.0	DRR334961	0:100.49 1:0	A:683370128;C:615324906;G:621209484;T:688756167;N:148	100	0			683370128	615324906	621209484	688756167	148	DRX323957	DRS217314	DRA013226	SINICA\|Machida Laboratory Biodiversity Research Center, Academia Sinica	SINICA\|Machida Laboratory Biodiversity Research Center, Academia Sinica	1	0.63764		0.04316		0.69656		0.48579		101		B		usable mapping rate	illumina	nextseq_v2	unknown	poly_a	nebnext	bulk	unknown	unknown	Taiwan	2021-12-23	Adult	Adult	Undetermined	Undetermined
31	31	DRR334960	DRX323956	DRS217301	DRP008001	PRJDB12578	Allometric scaling of RNA abundance from genes to communities	DRP008001	Other	The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole body RNA content in organisms. However testing RNA allometric scaling with next generation sequencing is yet to be done. Here we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling while the assumed temperature dependence appeared to be weak. Lastly allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes.		mRNA metatranscriptomic sequences from mock communities consist of five model species	mRNA mock community at 10 degrees rep 1	SAMD00422585		sample name:mRNA mock community 10 degrees rep 1\|biological replicate:1\|collection date:2021 01 15\|dev stage:Adult\|technical replicate:1\|temp:10\|treatment:mRNA	NextSeq 2000 sequencing of SAMD00422585	DRX323956	m10 1 mRNA.fastq	1	NEBNext Kit for Illumina		RNA-Seq	METATRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP008001	NextSeq 2000 sequencing of SAMD00422585				2879915507.0	28651533.0	DRR334960	0:100.52 1:0	A:761972464;C:675761096;G:678969165;T:763212637;N:145	100	0			761972464	675761096	678969165	763212637	145	DRX323956	DRS217301	DRA013226	SINICA\|Machida Laboratory Biodiversity Research Center, Academia Sinica	SINICA\|Machida Laboratory Biodiversity Research Center, Academia Sinica	1	0.47851		0.05671		0.72622		0.49269		101		B		usable mapping rate	illumina	nextseq_v2	unknown	poly_a	nebnext	bulk	unknown	unknown	Taiwan	2021-12-23	Adult	Adult	Undetermined	Undetermined
104	104	DRR189400	DRX179865	DRS200401	DRP003977	PRJDB4470	Gene expression analysis of the zebrafish brain	DRP003977	Other	Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.			Telencephalon of adult zebrafrish 30 min post test session of 1 day memory test in non trace 2 Way Active Avoidance coditioning 3	SAMD00182243		sample name:CSUS Tel 30 1d memory 3\|genotype:wild type\|tissue:brain	Illumina HiSeq 3000 sequencing of SAMD00182243	DRX179865	CSUS Tel 30 1d memory 3	1	SureSelect Strand Specific RNA Library Prep Kit		RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	Illumina HiSeq 3000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP003977	Illumina HiSeq 3000 sequencing of SAMD00182243				1340808120.0	37244670.0	DRR189400	0:36	A:330513975;C:306935584;G:320089399;T:383165274;N:103888	36				330513975	306935584	320089399	383165274	103888	DRX179865	DRS200401	DRA008864	NIG\|National Institute of Genetics (Japan)	National Institute of Genetics (Japan)	1	0.89272		0.19494		0.70335		0.49456		36		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Japan	2021-08-08	Adult	Adult	Brain	Nervous System
105	105	DRR189399	DRX179864	DRS200400	DRP003977	PRJDB4470	Gene expression analysis of the zebrafish brain	DRP003977	Other	Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.			Telencephalon of adult zebrafrish 30 min post test session of 1 day memory test in non trace 2 Way Active Avoidance coditioning 2	SAMD00182242		sample name:CSUS Tel 30 1d memory 2\|genotype:wild type\|tissue:brain	Illumina HiSeq 3000 sequencing of SAMD00182242	DRX179864	CSUS Tel 30 1d memory 2	1	SureSelect Strand Specific RNA Library Prep Kit		RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	Illumina HiSeq 3000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP003977	Illumina HiSeq 3000 sequencing of SAMD00182242				1279740096.0	35548336.0	DRR189399	0:36	A:314850837;C:294188093;G:304654881;T:365946483;N:99802	36				314850837	294188093	304654881	365946483	99802	DRX179864	DRS200400	DRA008864	NIG\|National Institute of Genetics (Japan)	National Institute of Genetics (Japan)	1	0.89485		0.18205		0.70593		0.49333		36		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Japan	2021-08-08	Adult	Adult	Brain	Nervous System
106	106	DRR189398	DRX179863	DRS200399	DRP003977	PRJDB4470	Gene expression analysis of the zebrafish brain	DRP003977	Other	Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.			Telencephalon of adult zebrafrish 30 min post test session of 1 day memory test in non trace 2 Way Active Avoidance coditioning 1	SAMD00182241		sample name:CSUS Tel 30 1d memory 1\|genotype:wild type\|tissue:brain	Illumina HiSeq 3000 sequencing of SAMD00182241	DRX179863	CSUS Tel 30 1d memory 1	1	SureSelect Strand Specific RNA Library Prep Kit		RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	Illumina HiSeq 3000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP003977	Illumina HiSeq 3000 sequencing of SAMD00182241				3012353100.0	83676475.0	DRR189398	0:36	A:740795057;C:693120664;G:717419185;T:860784745;N:233449	36				740795057	693120664	717419185	860784745	233449	DRX179863	DRS200399	DRA008864	NIG\|National Institute of Genetics (Japan)	National Institute of Genetics (Japan)	1	0.89676		0.1791		0.70569		0.49835		36		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Japan	2021-08-08	Adult	Adult	Brain	Nervous System
107	107	DRR189397	DRX179862	DRS200428	DRP003977	PRJDB4470	Gene expression analysis of the zebrafish brain	DRP003977	Other	Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.			Telencephalon of adult zebrafrish 60 min post exposure to the conditioning tank 3	SAMD00182240		sample name:Cont Tel 60 3\|genotype:wild type\|tissue:brain	Illumina HiSeq 3000 sequencing of SAMD00182240	DRX179862	Cont Tel 60 3	1	SureSelect Strand Specific RNA Library Prep Kit		RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	Illumina HiSeq 3000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP003977	Illumina HiSeq 3000 sequencing of SAMD00182240				5590147750.0	111802955.0	DRR189397	0:50	A:1365131560;C:1269631295;G:1366791321;T:1588422020;N:171554	50				1365131560	1269631295	1366791321	1588422020	171554	DRX179862	DRS200428	DRA008863	NIG\|National Institute of Genetics (Japan)	National Institute of Genetics (Japan)	1	0.89334		0.16354		0.7011		0.49383		50		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Japan	2021-08-08	Adult	Adult	Brain	Nervous System
108	108	DRR189396	DRX179861	DRS200427	DRP003977	PRJDB4470	Gene expression analysis of the zebrafish brain	DRP003977	Other	Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.			Telencephalon of adult zebrafrish 60 min post exposure to the conditioning tank 2	SAMD00182239		sample name:Cont Tel 60 2\|genotype:wild type\|tissue:brain	Illumina HiSeq 3000 sequencing of SAMD00182239	DRX179861	Cont Tel 60 2	1	SureSelect Strand Specific RNA Library Prep Kit		RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	Illumina HiSeq 3000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP003977	Illumina HiSeq 3000 sequencing of SAMD00182239				6429019650.0	128580393.0	DRR189396	0:50	A:1570141412;C:1457539089;G:1572785681;T:1828358007;N:195461	50				1570141412	1457539089	1572785681	1828358007	195461	DRX179861	DRS200427	DRA008863	NIG\|National Institute of Genetics (Japan)	National Institute of Genetics (Japan)	1	0.89595		0.16204		0.70743		0.49805		50		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Japan	2021-08-08	Adult	Adult	Brain	Nervous System
109	109	DRR189395	DRX179860	DRS200426	DRP003977	PRJDB4470	Gene expression analysis of the zebrafish brain	DRP003977	Other	Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.			Telencephalon of adult zebrafrish 60 min post exposure to the conditioning tank 1	SAMD00182238		sample name:Cont Tel 60 1\|genotype:wild type\|tissue:brain	Illumina HiSeq 3000 sequencing of SAMD00182238	DRX179860	Cont Tel 60 1	1	SureSelect Strand Specific RNA Library Prep Kit		RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	Illumina HiSeq 3000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP003977	Illumina HiSeq 3000 sequencing of SAMD00182238				6644185850.0	132883717.0	DRR189395	0:50	A:1637322491;C:1498943556;G:1616212676;T:1891505597;N:201530	50				1637322491	1498943556	1616212676	1891505597	201530	DRX179860	DRS200426	DRA008863	NIG\|National Institute of Genetics (Japan)	National Institute of Genetics (Japan)	1	0.89573		0.16421		0.7037		0.49805		50		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Japan	2021-08-08	Adult	Adult	Brain	Nervous System
110	110	DRR189394	DRX179859	DRS200407	DRP003977	PRJDB4470	Gene expression analysis of the zebrafish brain	DRP003977	Other	Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.			Telencephalon of adult zebrafrish 60 min post light stimulation in the conditioning tank 3	SAMD00182237		sample name:CS Tel 60 3\|genotype:wild type\|tissue:brain	Illumina HiSeq 3000 sequencing of SAMD00182237	DRX179859	CS Tel 60 3	1	SureSelect Strand Specific RNA Library Prep Kit		RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	Illumina HiSeq 3000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP003977	Illumina HiSeq 3000 sequencing of SAMD00182237				1387078956.0	38529971.0	DRR189394	0:36	A:333990578;C:315361737;G:337599372;T:400057968;N:69301	36				333990578	315361737	337599372	400057968	69301	DRX179859	DRS200407	DRA008862	NIG\|National Institute of Genetics (Japan)	National Institute of Genetics (Japan)	1	0.88133		0.18418		0.70747		0.4971		36		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Japan	2021-08-08	Adult	Adult	Brain	Nervous System
111	111	DRR189393	DRX179858	DRS200406	DRP003977	PRJDB4470	Gene expression analysis of the zebrafish brain	DRP003977	Other	Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.			Telencephalon of adult zebrafrish 60 min post light stimulation in the conditioning tank 2	SAMD00182236		sample name:CS Tel 60 2\|genotype:wild type\|tissue:brain	Illumina HiSeq 3000 sequencing of SAMD00182236	DRX179858	CS Tel 60 2	1	SureSelect Strand Specific RNA Library Prep Kit		RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	Illumina HiSeq 3000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP003977	Illumina HiSeq 3000 sequencing of SAMD00182236				537029424.0	14917484.0	DRR189393	0:36	A:127421487;C:122494467;G:132164579;T:154921150;N:27741	36				127421487	122494467	132164579	154921150	27741	DRX179858	DRS200406	DRA008862	NIG\|National Institute of Genetics (Japan)	National Institute of Genetics (Japan)	1	0.88264		0.17793		0.7083		0.49123		36		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Japan	2021-08-08	Adult	Adult	Brain	Nervous System
112	112	DRR189392	DRX179857	DRS200405	DRP003977	PRJDB4470	Gene expression analysis of the zebrafish brain	DRP003977	Other	Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.			Telencephalon of adult zebrafrish 60 min post light stimulation in the conditioning tank 1	SAMD00182235		sample name:CS Tel 60 1\|genotype:wild type\|tissue:brain	Illumina HiSeq 3000 sequencing of SAMD00182235	DRX179857	CS Tel 60 1	1	SureSelect Strand Specific RNA Library Prep Kit		RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	Illumina HiSeq 3000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP003977	Illumina HiSeq 3000 sequencing of SAMD00182235				3163663656.0	87879546.0	DRR189392	0:36	A:766146692;C:714108562;G:771785405;T:911468887;N:154110	36				766146692	714108562	771785405	911468887	154110	DRX179857	DRS200405	DRA008862	NIG\|National Institute of Genetics (Japan)	National Institute of Genetics (Japan)	1	0.88114		0.1803		0.7052		0.4917		36		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Japan	2021-08-08	Adult	Adult	Brain	Nervous System
113	113	DRR189391	DRX179856	DRS200404	DRP003977	PRJDB4470	Gene expression analysis of the zebrafish brain	DRP003977	Other	Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.			Telencephalon of adult zebrafrish 60 min post electrical shock delivery in the conditioning tank 3	SAMD00182234		sample name:US Tel 60 3\|genotype:wild type\|tissue:brain	Illumina HiSeq 3000 sequencing of SAMD00182234	DRX179856	US Tel 60 3	1	SureSelect Strand Specific RNA Library Prep Kit		RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	Illumina HiSeq 3000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP003977	Illumina HiSeq 3000 sequencing of SAMD00182234				1535884704.0	42663464.0	DRR189391	0:36	A:367444721;C:350978310;G:375524359;T:441859454;N:77860	36				367444721	350978310	375524359	441859454	77860	DRX179856	DRS200404	DRA008861	NIG\|National Institute of Genetics (Japan)	National Institute of Genetics (Japan)	1	0.88103		0.1788		0.7082		0.49462		36		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Japan	2021-08-08	Adult	Adult	Brain	Nervous System
114	114	DRR189390	DRX179855	DRS200403	DRP003977	PRJDB4470	Gene expression analysis of the zebrafish brain	DRP003977	Other	Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.			Telencephalon of adult zebrafrish 60 min post electrical shock delivery in the conditioning tank 2	SAMD00182233		sample name:US Tel 60 2\|genotype:wild type\|tissue:brain	Illumina HiSeq 3000 sequencing of SAMD00182233	DRX179855	US Tel 60 2	1	SureSelect Strand Specific RNA Library Prep Kit		RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	Illumina HiSeq 3000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP003977	Illumina HiSeq 3000 sequencing of SAMD00182233				737309916.0	20480831.0	DRR189390	0:36	A:176982713;C:168284406;G:179343270;T:212662841;N:36686	36				176982713	168284406	179343270	212662841	36686	DRX179855	DRS200403	DRA008861	NIG\|National Institute of Genetics (Japan)	National Institute of Genetics (Japan)	1	0.87995		0.18515		0.70816		0.49393		36		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Japan	2021-08-08	Adult	Adult	Brain	Nervous System
115	115	DRR189389	DRX179854	DRS200402	DRP003977	PRJDB4470	Gene expression analysis of the zebrafish brain	DRP003977	Other	Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.			Telencephalon of adult zebrafrish 60 min post electrical shock delivery in the conditioning tank 1	SAMD00182232		sample name:US Tel 60 1\|genotype:wild type\|tissue:brain	Illumina HiSeq 3000 sequencing of SAMD00182232	DRX179854	US Tel 60 1	1	SureSelect Strand Specific RNA Library Prep Kit		RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	Illumina HiSeq 3000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP003977	Illumina HiSeq 3000 sequencing of SAMD00182232				595837404.0	16551039.0	DRR189389	0:36	A:143956004;C:134783754;G:145443580;T:171624939;N:29127	36				143956004	134783754	145443580	171624939	29127	DRX179854	DRS200402	DRA008861	NIG\|National Institute of Genetics (Japan)	National Institute of Genetics (Japan)	1	0.87682		0.18328		0.70309		0.49081		36		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Japan	2021-08-08	Adult	Adult	Brain	Nervous System
116	116	DRR189388	DRX179853	DRS200452	DRP003977	PRJDB4470	Gene expression analysis of the zebrafish brain	DRP003977	Other	Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.			Telencephalon of adult zebrafrish 60 min post light and electrical shock association in non trace 2 Way Active Avoidance coditioning 3	SAMD00182231		sample name:CSUS Tel 60 3\|genotype:wild type\|tissue:brain	Illumina HiSeq 3000 sequencing of SAMD00182231	DRX179853	CSUS Tel 60 3	1	SureSelect Strand Specific RNA Library Prep Kit		RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	Illumina HiSeq 3000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP003977	Illumina HiSeq 3000 sequencing of SAMD00182231				608050044.0	16890279.0	DRR189388	0:36	A:145025778;C:137906052;G:149542672;T:175545338;N:30204	36				145025778	137906052	149542672	175545338	30204	DRX179853	DRS200452	DRA008860	NIG\|National Institute of Genetics (Japan)	National Institute of Genetics (Japan)	1	0.87983		0.18602		0.70445		0.49195		36		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Japan	2021-08-08	Adult	Adult	Brain	Nervous System
117	117	DRR189387	DRX179852	DRS200451	DRP003977	PRJDB4470	Gene expression analysis of the zebrafish brain	DRP003977	Other	Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.			Telencephalon of adult zebrafrish 60 min post light and electrical shock association in non trace 2 Way Active Avoidance coditioning 2	SAMD00182230		sample name:CSUS Tel 60 2\|genotype:wild type\|tissue:brain	Illumina HiSeq 3000 sequencing of SAMD00182230	DRX179852	CSUS Tel 60 2	1	SureSelect Strand Specific RNA Library Prep Kit		RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	Illumina HiSeq 3000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP003977	Illumina HiSeq 3000 sequencing of SAMD00182230				777589452.0	21599707.0	DRR189387	0:36	A:185463269;C:177742981;G:190443063;T:223900096;N:40043	36				185463269	177742981	190443063	223900096	40043	DRX179852	DRS200451	DRA008860	NIG\|National Institute of Genetics (Japan)	National Institute of Genetics (Japan)	1	0.88331		0.17918		0.70516		0.48956		36		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Japan	2021-08-08	Adult	Adult	Brain	Nervous System
118	118	DRR189386	DRX179851	DRS200450	DRP003977	PRJDB4470	Gene expression analysis of the zebrafish brain	DRP003977	Other	Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.			Telencephalon of adult zebrafrish 60 min post light and electrical shock association in non trace 2 Way Active Avoidance coditioning 1	SAMD00182229		sample name:CSUS Tel 60 1\|genotype:wild type\|tissue:brain	Illumina HiSeq 3000 sequencing of SAMD00182229	DRX179851	CSUS Tel 60 1	1	SureSelect Strand Specific RNA Library Prep Kit		RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	Illumina HiSeq 3000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP003977	Illumina HiSeq 3000 sequencing of SAMD00182229				2738622348.0	76072843.0	DRR189386	0:36	A:662989485;C:622023190;G:663013857;T:790459930;N:135886	36				662989485	622023190	663013857	790459930	135886	DRX179851	DRS200450	DRA008860	NIG\|National Institute of Genetics (Japan)	National Institute of Genetics (Japan)	1	0.87743		0.19164		0.70025		0.49073		36		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Japan	2021-08-08	Adult	Adult	Brain	Nervous System
119	119	DRR189385	DRX179850	DRS200435	DRP003977	PRJDB4470	Gene expression analysis of the zebrafish brain	DRP003977	Other	Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.			Telencephalon of EMX3 / adult zebrafish 3	SAMD00182228		sample name:Emx3 Adult Tel 3\|genotype:Emx3 / \|tissue:brain	Illumina HiSeq 3000 sequencing of SAMD00182228	DRX179850	Emx3 / Adult Tel 3	1	SureSelect Strand Specific RNA Library Prep Kit		RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	Illumina HiSeq 3000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP003977	Illumina HiSeq 3000 sequencing of SAMD00182228				1323636552.0	36767682.0	DRR189385	0:36	A:309582925;C:310206951;G:325673647;T:378136039;N:36990	36				309582925	310206951	325673647	378136039	36990	DRX179850	DRS200435	DRA008859	NIG\|National Institute of Genetics (Japan)	National Institute of Genetics (Japan)	1	0.8932		0.19244		0.71334		0.50591		36		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Japan	2021-08-08	Adult	Adult	Brain	Nervous System
120	120	DRR189384	DRX179849	DRS200434	DRP003977	PRJDB4470	Gene expression analysis of the zebrafish brain	DRP003977	Other	Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.			Telencephalon of EMX3 / adult zebrafish 2	SAMD00182227		sample name:Emx3 Adult Tel 2\|genotype:Emx3 / \|tissue:brain	Illumina HiSeq 3000 sequencing of SAMD00182227	DRX179849	Emx3 / Adult Tel 2	1	SureSelect Strand Specific RNA Library Prep Kit		RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	Illumina HiSeq 3000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP003977	Illumina HiSeq 3000 sequencing of SAMD00182227				2994105168.0	83169588.0	DRR189384	0:36	A:709730692;C:691531995;G:727245229;T:865514929;N:82323	36				709730692	691531995	727245229	865514929	82323	DRX179849	DRS200434	DRA008859	NIG\|National Institute of Genetics (Japan)	National Institute of Genetics (Japan)	1	0.90382		0.1826		0.70197		0.49719		36		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Japan	2021-08-08	Adult	Adult	Brain	Nervous System
121	121	DRR189383	DRX179848	DRS200433	DRP003977	PRJDB4470	Gene expression analysis of the zebrafish brain	DRP003977	Other	Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.			Telencephalon of EMX3 / adult zebrafish 1	SAMD00182226		sample name:Emx3 Adult Tel 1\|genotype:Emx3 / \|tissue:brain	Illumina HiSeq 3000 sequencing of SAMD00182226	DRX179848	Emx3 / Adult Tel 1	1	SureSelect Strand Specific RNA Library Prep Kit		RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	Illumina HiSeq 3000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP003977	Illumina HiSeq 3000 sequencing of SAMD00182226				1151464896.0	31985136.0	DRR189383	0:36	A:272427216;C:266708394;G:280781178;T:331515997;N:32111	36				272427216	266708394	280781178	331515997	32111	DRX179848	DRS200433	DRA008859	NIG\|National Institute of Genetics (Japan)	National Institute of Genetics (Japan)	1	0.89942		0.17402		0.70364		0.49438		36		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Japan	2021-08-08	Adult	Adult	Brain	Nervous System
122	122	DRR189382	DRX179847	DRS200421	DRP003977	PRJDB4470	Gene expression analysis of the zebrafish brain	DRP003977	Other	Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.			Telencephalon of wild type adult zebrafish 3	SAMD00182225		sample name:WT Adult Tel 3\|genotype:wild type\|tissue:brain	Illumina HiSeq 3000 sequencing of SAMD00182225	DRX179847	WT Adult Tel 3	1	SureSelect Strand Specific RNA Library Prep Kit		RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	Illumina HiSeq 3000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP003977	Illumina HiSeq 3000 sequencing of SAMD00182225				2837488824.0	78819134.0	DRR189382	0:36	A:678395895;C:655098137;G:687520693;T:816395518;N:78581	36				678395895	655098137	687520693	816395518	78581	DRX179847	DRS200421	DRA008858	NIG\|National Institute of Genetics (Japan)	National Institute of Genetics (Japan)	1	0.89483		0.18623		0.70544		0.49839		36		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Japan	2021-08-08	Adult	Adult	Brain	Nervous System
123	123	DRR189381	DRX179846	DRS200420	DRP003977	PRJDB4470	Gene expression analysis of the zebrafish brain	DRP003977	Other	Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.			Telencephalon of wild type adult zebrafish 2	SAMD00182224		sample name:WT Adult Tel 2\|genotype:wild type\|tissue:brain	Illumina HiSeq 3000 sequencing of SAMD00182224	DRX179846	WT Adult Tel 2	1	SureSelect Strand Specific RNA Library Prep Kit		RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	Illumina HiSeq 3000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP003977	Illumina HiSeq 3000 sequencing of SAMD00182224				1456800264.0	40466674.0	DRR189381	0:36	A:345320431;C:336838149;G:356264798;T:418336552;N:40334	36				345320431	336838149	356264798	418336552	40334	DRX179846	DRS200420	DRA008858	NIG\|National Institute of Genetics (Japan)	National Institute of Genetics (Japan)	1	0.89496		0.18691		0.70802		0.49721		36		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Japan	2021-08-08	Adult	Adult	Brain	Nervous System
124	124	DRR189380	DRX179845	DRS200419	DRP003977	PRJDB4470	Gene expression analysis of the zebrafish brain	DRP003977	Other	Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.			Telencephalon of wild type adult zebrafish 1	SAMD00182223		sample name:WT Adult Tel 1\|genotype:wild type\|tissue:brain	Illumina HiSeq 3000 sequencing of SAMD00182223	DRX179845	WT Adult Tel 1	1	SureSelect Strand Specific RNA Library Prep Kit		RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	Illumina HiSeq 3000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP003977	Illumina HiSeq 3000 sequencing of SAMD00182223				2533282452.0	70368957.0	DRR189380	0:36	A:602595083;C:585466052;G:616064286;T:729086926;N:70105	36				602595083	585466052	616064286	729086926	70105	DRX179845	DRS200419	DRA008858	NIG\|National Institute of Genetics (Japan)	National Institute of Genetics (Japan)	1	0.89412		0.19005		0.70816		0.49843		36		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Japan	2021-08-08	Adult	Adult	Brain	Nervous System
174	174	DRR084198	DRX078029	DRS086523	DRP004758	PRJDB5490	Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish	DRP004758	Other	Two essential processes oocyte maturation and ovulation before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid 17 20 beta dihydroxy 4 pregnen 3 one 17 20 beta DHP in teleost the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.		in vivo testosterone treatment	zebrafish ovary isolated from adult fish in vivo testoster1 treatment. [RNAseq replicate2]	SAMD00073605		sample name:TES1 4th\|replicate:biological replicate 2	Illumina HiSeq 2500 sequencing of SAMD00073605	DRX078029	zebrafish ovary isolated from adult fish in vivo testosterone treatment. [RNAseq replicate2]	1	Agilent SureSelect Strand Specific RNA Prep Kit		RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP004758	Illumina HiSeq 2500 sequencing of SAMD00073605				1382763132.0	38410087.0	DRR084198	0:36	A:314367195;C:333340483;G:353519828;T:378654329;N:2881297	36				314367195	333340483	353519828	378654329	2881297	DRX078029	DRS086523	DRA005484	SHIZUOKA\|Shizuoka University	Shizuoka University	1	0.90366		0.02033		0.77104		0.46543		36		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Japan	2019-01-23	Adult	Adult	Gonad	Reproductive System
176	176	DRR084196	DRX078027	DRS086521	DRP004758	PRJDB5490	Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish	DRP004758	Other	Two essential processes oocyte maturation and ovulation before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid 17 20 beta dihydroxy 4 pregnen 3 one 17 20 beta DHP in teleost the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.		in vivo ethanol treatment	zebrafish ovary isolated from adult fish in vivo ethanol treatment. [RNAseq replicate2]	SAMD00073603		sample name:Et 4th\|replicate:biological replicate 2	Illumina HiSeq 2500 sequencing of SAMD00073603	DRX078027	zebrafish ovary isolated from adult fish in vivo ethanol treatment. [RNAseq replicate2]	1	Agilent SureSelect Strand Specific RNA Prep Kit		RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP004758	Illumina HiSeq 2500 sequencing of SAMD00073603				1456791660.0	40466435.0	DRR084196	0:36	A:336533534;C:355126203;G:368021063;T:394179246;N:2931614	36				336533534	355126203	368021063	394179246	2931614	DRX078027	DRS086521	DRA005484	SHIZUOKA\|Shizuoka University	Shizuoka University	1	0.89408		0.02082		0.77027		0.45866		36		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Japan	2019-01-23	Adult	Adult	Gonad	Reproductive System
177	177	DRR084195	DRX078026	DRS086520	DRP004758	PRJDB5490	Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish	DRP004758	Other	Two essential processes oocyte maturation and ovulation before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid 17 20 beta dihydroxy 4 pregnen 3 one 17 20 beta DHP in teleost the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.		natural paring late sample	zebrafish ovary isolated from adult fish natural paring ovulation. [RNAseq replicate2]	SAMD00073602		sample name:O 4th\|replicate:biological replicate 2	Illumina HiSeq 2500 sequencing of SAMD00073602	DRX078026	zebrafish ovary isolated from adult fish natural paring ovulation. [RNAseq replicate2]	1	Agilent SureSelect Strand Specific RNA Prep Kit		RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP004758	Illumina HiSeq 2500 sequencing of SAMD00073602				1627945092.0	45220697.0	DRR084195	0:36	A:381205209;C:392853175;G:410714269;T:439790560;N:3381879	36				381205209	392853175	410714269	439790560	3381879	DRX078026	DRS086520	DRA005484	SHIZUOKA\|Shizuoka University	Shizuoka University	1	0.89419		0.02159		0.76848		0.46407		36		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Japan	2019-01-23	Adult	Adult	Gonad	Reproductive System
178	178	DRR084194	DRX078025	DRS086519	DRP004758	PRJDB5490	Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish	DRP004758	Other	Two essential processes oocyte maturation and ovulation before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid 17 20 beta dihydroxy 4 pregnen 3 one 17 20 beta DHP in teleost the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.		in vivo maturation inducing hormone DHP treatment	zebrafish ovary isolated from adult fish in vivo maturation inducing horm1 DHP treatment. [RNAseq replicate2]	SAMD00073601		sample name:DHP 4th\|replicate:biological replicate 2	Illumina HiSeq 2500 sequencing of SAMD00073601	DRX078025	zebrafish ovary isolated from adult fish in vivo maturation inducing hormone DHP treatment. [RNAseq replicate2]	1	Agilent SureSelect Strand Specific RNA Prep Kit		RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP004758	Illumina HiSeq 2500 sequencing of SAMD00073601				969680196.0	26935561.0	DRR084194	0:36	A:223558856;C:233793515;G:244712298;T:265549055;N:2066472	36				223558856	233793515	244712298	265549055	2066472	DRX078025	DRS086519	DRA005484	SHIZUOKA\|Shizuoka University	Shizuoka University	1	0.90178		0.02203		0.76579		0.46491		36		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Japan	2019-01-23	Adult	Adult	Gonad	Reproductive System
179	179	DRR084193	DRX078024	DRS086518	DRP004758	PRJDB5490	Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish	DRP004758	Other	Two essential processes oocyte maturation and ovulation before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid 17 20 beta dihydroxy 4 pregnen 3 one 17 20 beta DHP in teleost the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.		in vivo diethylstilbestrol DES treatment	zebrafish ovary isolated from adult fish in vivo diethylstilbestrol DES treatment. [RNAseq replicate2]	SAMD00073600		sample name:DES 4th\|replicate:biological replicate 2	Illumina HiSeq 2500 sequencing of SAMD00073600	DRX078024	zebrafish ovary isolated from adult fish in vivo diethylstilbestrol DES treatment. [RNAseq replicate2]	1	Agilent SureSelect Strand Specific RNA Prep Kit		RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP004758	Illumina HiSeq 2500 sequencing of SAMD00073600				825301296.0	22925036.0	DRR084193	0:36	A:189771874;C:198593952;G:209666041;T:225480165;N:1789264	36				189771874	198593952	209666041	225480165	1789264	DRX078024	DRS086518	DRA005484	SHIZUOKA\|Shizuoka University	Shizuoka University	1	0.90036		0.0197		0.7721		0.45773		36		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Japan	2019-01-23	Adult	Adult	Gonad	Reproductive System
180	180	DRR084192	DRX078023	DRS086517	DRP004758	PRJDB5490	Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish	DRP004758	Other	Two essential processes oocyte maturation and ovulation before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid 17 20 beta dihydroxy 4 pregnen 3 one 17 20 beta DHP in teleost the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.		natural paring late sample	zebrafish ovary isolated from adult fish natural paring ovulation. [RNAseq replicate1]	SAMD00073599		sample name:O\|replicate:biological replicate 1	Illumina HiSeq 2500 sequencing of SAMD00073599	DRX078023	zebrafish ovary isolated from adult fish natural paring ovulation. [RNAseq replicate1]	1	Agilent SureSelect Strand Specific RNA Prep Kit		RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP004758	Illumina HiSeq 2500 sequencing of SAMD00073599				1474870356.0	40968621.0	DRR084192	0:36	A:334130826;C:361572335;G:369758908;T:409173431;N:234856	36				334130826	361572335	369758908	409173431	234856	DRX078023	DRS086517	DRA005484	SHIZUOKA\|Shizuoka University	Shizuoka University	1	0.91516		0.02086		0.76792		0.47914		36		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Japan	2019-01-23	Adult	Adult	Gonad	Reproductive System
182	182	DRR084190	DRX078021	DRS086515	DRP004758	PRJDB5490	Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish	DRP004758	Other	Two essential processes oocyte maturation and ovulation before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid 17 20 beta dihydroxy 4 pregnen 3 one 17 20 beta DHP in teleost the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.		in vivo maturation inducing hormone DHP treatment	zebrafish ovary isolated from adult fish in vivo maturation inducing horm1 DHP treatment. [RNAseq replicate1]	SAMD00073597		sample name:DHP\|replicate:biological replicate 1	Illumina HiSeq 2500 sequencing of SAMD00073597	DRX078021	zebrafish ovary isolated from adult fish in vivo maturation inducing hormone DHP treatment. [RNAseq replicate1]	1	Agilent SureSelect Strand Specific RNA Prep Kit		RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP004758	Illumina HiSeq 2500 sequencing of SAMD00073597				1527194556.0	42422071.0	DRR084190	0:36	A:352068936;C:371030475;G:383086948;T:420761508;N:246689	36				352068936	371030475	383086948	420761508	246689	DRX078021	DRS086515	DRA005484	SHIZUOKA\|Shizuoka University	Shizuoka University	1	0.91815		0.02248		0.76209		0.46867		36		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Japan	2019-01-23	Adult	Adult	Gonad	Reproductive System
183	183	DRR084189	DRX078020	DRS086514	DRP004758	PRJDB5490	Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish	DRP004758	Other	Two essential processes oocyte maturation and ovulation before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid 17 20 beta dihydroxy 4 pregnen 3 one 17 20 beta DHP in teleost the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.		in vivo testosterone treatment	zebrafish ovary isolated from adult fish in vivo testoster1 treatment. [RNAseq replicate1]	SAMD00073596		sample name:TES\|replicate:biological replicate 1	Illumina HiSeq 2500 sequencing of SAMD00073596	DRX078020	zebrafish ovary isolated from adult fish in vivo testosterone treatment. [RNAseq replicate1]	1	Agilent SureSelect Strand Specific RNA Prep Kit		RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP004758	Illumina HiSeq 2500 sequencing of SAMD00073596				1403618796.0	38989411.0	DRR084189	0:36	A:321063874;C:342718133;G:352434647;T:387171455;N:230687	36				321063874	342718133	352434647	387171455	230687	DRX078020	DRS086514	DRA005484	SHIZUOKA\|Shizuoka University	Shizuoka University	1	0.91583		0.02212		0.76073		0.47596		36		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Japan	2019-01-23	Adult	Adult	Gonad	Reproductive System
184	184	DRR084188	DRX078019	DRS086513	DRP004758	PRJDB5490	Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish	DRP004758	Other	Two essential processes oocyte maturation and ovulation before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid 17 20 beta dihydroxy 4 pregnen 3 one 17 20 beta DHP in teleost the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.		in vivo diethylstilbestrol DES treatment	zebrafish ovary isolated from adult fish in vivo diethylstilbestrol DES treatment. [RNAseq replicate1]	SAMD00073595		sample name:DES\|replicate:biological replicate 1	Illumina HiSeq 2500 sequencing of SAMD00073595	DRX078019	zebrafish ovary isolated from adult fish in vivo diethylstilbestrol DES treatment. [RNAseq replicate1]	1	Agilent SureSelect Strand Specific RNA Prep Kit		RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP004758	Illumina HiSeq 2500 sequencing of SAMD00073595				1532053512.0	42557042.0	DRR084188	0:36	A:342701220;C:372650449;G:392432461;T:424025702;N:243680	36				342701220	372650449	392432461	424025702	243680	DRX078019	DRS086513	DRA005484	SHIZUOKA\|Shizuoka University	Shizuoka University	1	0.91276		0.01965		0.77358		0.46461		36		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Japan	2019-01-23	Adult	Adult	Gonad	Reproductive System
185	185	DRR084187	DRX078018	DRS086512	DRP004758	PRJDB5490	Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish	DRP004758	Other	Two essential processes oocyte maturation and ovulation before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid 17 20 beta dihydroxy 4 pregnen 3 one 17 20 beta DHP in teleost the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.		in vivo ethanol treatment	zebrafish ovary isolated from adult fish in vivo ethanol treatment. [RNAseq replicate1]	SAMD00073594		sample name:EtOH\|replicate:biological replicate 1	Illumina HiSeq 2500 sequencing of SAMD00073594	DRX078018	zebrafish ovary isolated from adult fish in vivo ethanol treatment. [RNAseq replicate1]	1	Agilent SureSelect Strand Specific RNA Prep Kit		RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP004758	Illumina HiSeq 2500 sequencing of SAMD00073594				1152032724.0	32000909.0	DRR084187	0:36	A:265166034;C:279617628;G:285136940;T:321928656;N:183466	36				265166034	279617628	285136940	321928656	183466	DRX078018	DRS086512	DRA005484	SHIZUOKA\|Shizuoka University	Shizuoka University	1	0.90791		0.02405		0.75972		0.48931		36		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Japan	2019-01-23	Adult	Adult	Gonad	Reproductive System
288	288	DRR224554	DRX214839	DRS236362	DRP008458	PRJDB9741	RNA seq for developing pectoral fin in zebrafish	DRP008458	Other	From the developmental view of fin to limb transition an important event in vertebrate evolution we seek fish specific genes that show characteristic expression pattern in the developing fin.			pectoral fin from RIKEN Wild type zebrafish Adult C	SAMD00222585		sample name:Adult C	Illumina NovaSeq 6000 paired end sequencing of SAMD00222585	DRX214839	Adult C	1	Illumina TruSeq Stranded mRNA Library Prep Kit		RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP008458	Illumina NovaSeq 6000 paired end sequencing of SAMD00222585				11727505800.0	58637529.0	DRR224554	0:100 1:100	A:3137648588;C:2705013210;G:3191753451;T:2692963496;N:127055	100	100			3137648588	2705013210	3191753451	2692963496	127055	DRX214839	DRS236362	DRA010086	TOHOKUGL\|Laboratory of organ morphogenesis	Graduate School of Life Sciences, Tohoku University	2	0.95934	0.93156	0.03853	0.0394	0.72683	0.74625	0.45812	0.47098	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	Japan	2022-04-21	Adult	Adult	Fin	Surface Structure
289	289	DRR224553	DRX214838	DRS236361	DRP008458	PRJDB9741	RNA seq for developing pectoral fin in zebrafish	DRP008458	Other	From the developmental view of fin to limb transition an important event in vertebrate evolution we seek fish specific genes that show characteristic expression pattern in the developing fin.			pectoral fin from RIKEN Wild type zebrafish Adult B	SAMD00222584		sample name:Adult B	Illumina NovaSeq 6000 paired end sequencing of SAMD00222584	DRX214838	Adult B	1	Illumina TruSeq Stranded mRNA Library Prep Kit		RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP008458	Illumina NovaSeq 6000 paired end sequencing of SAMD00222584				22010855600.0	110054278.0	DRR224553	0:100 1:100	A:5511440112;C:5498539659;G:5546758172;T:5453879750;N:237907	100	100			5511440112	5498539659	5546758172	5453879750	237907	DRX214838	DRS236361	DRA010086	TOHOKUGL\|Laboratory of organ morphogenesis	Graduate School of Life Sciences, Tohoku University	2	0.95774	0.95394	0.04568	0.04411	0.70701	0.70881	0.47041	0.47938	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	Japan	2022-04-21	Adult	Adult	Fin	Surface Structure
290	290	DRR224552	DRX214837	DRS236360	DRP008458	PRJDB9741	RNA seq for developing pectoral fin in zebrafish	DRP008458	Other	From the developmental view of fin to limb transition an important event in vertebrate evolution we seek fish specific genes that show characteristic expression pattern in the developing fin.			pectoral fin from RIKEN Wild type zebrafish Adult A	SAMD00222583		sample name:Adult A	Illumina NovaSeq 6000 paired end sequencing of SAMD00222583	DRX214837	Adult A	1	Illumina TruSeq Stranded mRNA Library Prep Kit		RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP008458	Illumina NovaSeq 6000 paired end sequencing of SAMD00222583				17683281000.0	88416405.0	DRR224552	0:100 1:100	A:4386756926;C:4479415938;G:4578796094;T:4238125580;N:186462	100	100			4386756926	4479415938	4578796094	4238125580	186462	DRX214837	DRS236360	DRA010086	TOHOKUGL\|Laboratory of organ morphogenesis	Graduate School of Life Sciences, Tohoku University	2	0.95974	0.95566	0.05237	0.05086	0.74357	0.74742	0.48578	0.49971	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	Japan	2022-04-21	Adult	Adult	Fin	Surface Structure
9702	9702	ERR3301003	ERX3327070	ERS3389658	ERP115040	PRJEB32363	RNA seq of zebrafish sa12692 mutants against WT controls	E-MTAB-7920	Transcriptome Analysis	Arrhythmogenic Right Ventricular Cardiomyopathy is a congenital heart disorder characterized by fibrofatty replacement of the myocardium. The exact molecular mechanisms underlying the disease remain to be elucidated and treatment options are limited. The sa12692 mutant line contains a splice site mutation in the plakoglobin gene resulting in the expression of a truncated protein. This protein is highly similar to the protein expressed in Naxos disease a recessive form of ARVC. RNA seq was used to investigate the effect of the sa12692 mutation on gene expression in order to uncover signalling pathways involved in the pathogenesis of ARVC. Gene expression was examined in whole larvae at 5 dpf and in hearts of 1 year old adult fish. Larvae at 5 dpf were selected as this timepoint is equivalent to birth in humans. Adult hearts were selected as ARVC is a disorder of the heart and cardiac symptoms generally manifest in maturity. Hence the molecular effect of the mutation could be profiled at two life stages.	ENA FIRST PUBLIC:2021 04 30\|ENA LAST UPDATE:2019 04 30	Protocols: Each adult fish was euthanized using MS 222 and secured ventral side up in a Petri dish. A micro scissors was used to make an incision from the base of one pectoral fin to the other. A second incision was made from the centre of the first incision to the gill area. Fine needles were used to pin back the chest wall and expose the heart. The ventricle atrium and bulbus arteriosus were located. The bulbus arteriosus was cut to detach it from the gills. The entire intact heart was removed by pinching the bulbus arteriosus with a forceps and making one final cut between the atrium and sinus venosus. For RNA extractions hearts were rinsed in sterile PBS and stored in RNAlater® until use. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend th…	WT heart rep 3	SAMEA5585434	Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway	ENA FIRST PUBLIC:2021 04 30T00:25:03Z\|ENA LAST UPDATE:2019 04 30T15:21:47Z\|External Id:SAMEA5585434\|INSDC center name:Dept. of Pharmacology and Therapeutics College of Medicine Nursing and Heath Sciences National University of Ireland Galway\|INSDC first public:2021 04 30T00:25:03Z\|INSDC last update:2019 04 30T15:21:47Z\|INSDC status:public\|Submitter Id:E MTAB 7920:WT heart rep 3\|age:1\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|disease:normal\|genotype:wild type genotype\|individual:6\|organism part:heart\|sample name:E MTAB 7920:WT heart rep 3\|scientific name:Danio rerio\|sex:female\|strain:AB	NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls	E MTAB 7920:WT heart rep 3 p	WT heart rep 3 p	RNA seq of zebrafish sa12692 mutants against WT controls	Each adult fish was euthanized using MS 222 and secured ventral side up in a Petri dish. A micro scissors was used to make an incision from the base of one pectoral fin to the other. A second incision was made from the centre of the first incision to the gill area. Fine needles were used to pin back the chest wall and expose the heart. The ventricle atrium and bulbus arteriosus were located. The bulbus arteriosus was cut to detach it from the gills. The entire intact heart was removed by pinching the bulbus arteriosus with a forceps and making one final cut between the atrium and sinus venosus. For RNA extractions hearts were rinsed in sterile PBS and stored in RNAlater® until use. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. T…	Experimental Factor: genotype:wild type genotype\|Experimental Factor: developmental stage:adult\|Experimental Factor: organism part:heart	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	NextSeq 500		ERP115040	NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls	ENA FIRST PUBLIC:2021 04 30\|ENA LAST UPDATE:2019 04 30	HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1WTheart3_1.fq.gz HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1WTheart3_2.fq.gz	fastq fastq	7339830080.0	45873938.0	E MTAB 7920:HJGMYBGX2 Zebrafish mRNA 17s001029 1 1 Morris lane1WTheart3	0:80 1:80	A:1985328994;C:1673818891;G:1695753386;T:1984031668;N:897141	80	80			1985328994	1673818891	1695753386	1984031668	897141	ERX3327070	ERS3389658	ERA1880314	Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway\|European Nucleotide Archive	Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway\|European Nucleotide Archive	2	0.9311	0.94858	0.07774	0.07789	0.76378	0.76394	0.52815	0.52065	80	80	B	B	biological fallback assumption	illumina	nextseq	3prime	poly_a	trueseq	bulk	bulk	bulk	Ireland	2019-04-30	Adult	Adult	Multi-tissue	Multi-system
9703	9703	ERR3301002	ERX3327069	ERS3389657	ERP115040	PRJEB32363	RNA seq of zebrafish sa12692 mutants against WT controls	E-MTAB-7920	Transcriptome Analysis	Arrhythmogenic Right Ventricular Cardiomyopathy is a congenital heart disorder characterized by fibrofatty replacement of the myocardium. The exact molecular mechanisms underlying the disease remain to be elucidated and treatment options are limited. The sa12692 mutant line contains a splice site mutation in the plakoglobin gene resulting in the expression of a truncated protein. This protein is highly similar to the protein expressed in Naxos disease a recessive form of ARVC. RNA seq was used to investigate the effect of the sa12692 mutation on gene expression in order to uncover signalling pathways involved in the pathogenesis of ARVC. Gene expression was examined in whole larvae at 5 dpf and in hearts of 1 year old adult fish. Larvae at 5 dpf were selected as this timepoint is equivalent to birth in humans. Adult hearts were selected as ARVC is a disorder of the heart and cardiac symptoms generally manifest in maturity. Hence the molecular effect of the mutation could be profiled at two life stages.	ENA FIRST PUBLIC:2021 04 30\|ENA LAST UPDATE:2019 04 30	Protocols: Each adult fish was euthanized using MS 222 and secured ventral side up in a Petri dish. A micro scissors was used to make an incision from the base of one pectoral fin to the other. A second incision was made from the centre of the first incision to the gill area. Fine needles were used to pin back the chest wall and expose the heart. The ventricle atrium and bulbus arteriosus were located. The bulbus arteriosus was cut to detach it from the gills. The entire intact heart was removed by pinching the bulbus arteriosus with a forceps and making one final cut between the atrium and sinus venosus. For RNA extractions hearts were rinsed in sterile PBS and stored in RNAlater® until use. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend th…	WT heart rep 2	SAMEA5585433	Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway	ENA FIRST PUBLIC:2021 04 30T00:25:03Z\|ENA LAST UPDATE:2019 04 30T15:21:47Z\|External Id:SAMEA5585433\|INSDC center name:Dept. of Pharmacology and Therapeutics College of Medicine Nursing and Heath Sciences National University of Ireland Galway\|INSDC first public:2021 04 30T00:25:03Z\|INSDC last update:2019 04 30T15:21:47Z\|INSDC status:public\|Submitter Id:E MTAB 7920:WT heart rep 2\|age:1\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|disease:normal\|genotype:wild type genotype\|individual:5\|organism part:heart\|sample name:E MTAB 7920:WT heart rep 2\|scientific name:Danio rerio\|sex:female\|strain:AB	NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls	E MTAB 7920:WT heart rep 2 p	WT heart rep 2 p	RNA seq of zebrafish sa12692 mutants against WT controls	Each adult fish was euthanized using MS 222 and secured ventral side up in a Petri dish. A micro scissors was used to make an incision from the base of one pectoral fin to the other. A second incision was made from the centre of the first incision to the gill area. Fine needles were used to pin back the chest wall and expose the heart. The ventricle atrium and bulbus arteriosus were located. The bulbus arteriosus was cut to detach it from the gills. The entire intact heart was removed by pinching the bulbus arteriosus with a forceps and making one final cut between the atrium and sinus venosus. For RNA extractions hearts were rinsed in sterile PBS and stored in RNAlater® until use. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. T…	Experimental Factor: genotype:wild type genotype\|Experimental Factor: developmental stage:adult\|Experimental Factor: organism part:heart	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	NextSeq 500		ERP115040	NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls	ENA FIRST PUBLIC:2021 04 30\|ENA LAST UPDATE:2019 04 30	HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1WTheart2_1.fq.gz HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1WTheart2_2.fq.gz	fastq fastq	7486415840.0	46790099.0	E MTAB 7920:HJGMYBGX2 Zebrafish mRNA 17s001029 1 1 Morris lane1WTheart2	0:80 1:80	A:2020798219;C:1702752807;G:1731176796;T:2030756525;N:931493	80	80			2020798219	1702752807	1731176796	2030756525	931493	ERX3327069	ERS3389657	ERA1880314	Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway\|European Nucleotide Archive	Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway\|European Nucleotide Archive	2	0.93397	0.9509	0.07752	0.07859	0.76019	0.76002	0.54034	0.54728	80	80	B	B	biological fallback assumption	illumina	nextseq	3prime	poly_a	trueseq	bulk	bulk	bulk	Ireland	2019-04-30	Adult	Adult	Multi-tissue	Multi-system
9704	9704	ERR3301001	ERX3327068	ERS3389656	ERP115040	PRJEB32363	RNA seq of zebrafish sa12692 mutants against WT controls	E-MTAB-7920	Transcriptome Analysis	Arrhythmogenic Right Ventricular Cardiomyopathy is a congenital heart disorder characterized by fibrofatty replacement of the myocardium. The exact molecular mechanisms underlying the disease remain to be elucidated and treatment options are limited. The sa12692 mutant line contains a splice site mutation in the plakoglobin gene resulting in the expression of a truncated protein. This protein is highly similar to the protein expressed in Naxos disease a recessive form of ARVC. RNA seq was used to investigate the effect of the sa12692 mutation on gene expression in order to uncover signalling pathways involved in the pathogenesis of ARVC. Gene expression was examined in whole larvae at 5 dpf and in hearts of 1 year old adult fish. Larvae at 5 dpf were selected as this timepoint is equivalent to birth in humans. Adult hearts were selected as ARVC is a disorder of the heart and cardiac symptoms generally manifest in maturity. Hence the molecular effect of the mutation could be profiled at two life stages.	ENA FIRST PUBLIC:2021 04 30\|ENA LAST UPDATE:2019 04 30	Protocols: Each adult fish was euthanized using MS 222 and secured ventral side up in a Petri dish. A micro scissors was used to make an incision from the base of one pectoral fin to the other. A second incision was made from the centre of the first incision to the gill area. Fine needles were used to pin back the chest wall and expose the heart. The ventricle atrium and bulbus arteriosus were located. The bulbus arteriosus was cut to detach it from the gills. The entire intact heart was removed by pinching the bulbus arteriosus with a forceps and making one final cut between the atrium and sinus venosus. For RNA extractions hearts were rinsed in sterile PBS and stored in RNAlater® until use. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend th…	WT heart rep 1	SAMEA5585432	Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway	ENA FIRST PUBLIC:2021 04 30T00:25:03Z\|ENA LAST UPDATE:2019 04 30T15:21:47Z\|External Id:SAMEA5585432\|INSDC center name:Dept. of Pharmacology and Therapeutics College of Medicine Nursing and Heath Sciences National University of Ireland Galway\|INSDC first public:2021 04 30T00:25:03Z\|INSDC last update:2019 04 30T15:21:47Z\|INSDC status:public\|Submitter Id:E MTAB 7920:WT heart rep 1\|age:1\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|disease:normal\|genotype:wild type genotype\|individual:4\|organism part:heart\|sample name:E MTAB 7920:WT heart rep 1\|scientific name:Danio rerio\|sex:female\|strain:AB	NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls	E MTAB 7920:WT heart rep 1 p	WT heart rep 1 p	RNA seq of zebrafish sa12692 mutants against WT controls	Each adult fish was euthanized using MS 222 and secured ventral side up in a Petri dish. A micro scissors was used to make an incision from the base of one pectoral fin to the other. A second incision was made from the centre of the first incision to the gill area. Fine needles were used to pin back the chest wall and expose the heart. The ventricle atrium and bulbus arteriosus were located. The bulbus arteriosus was cut to detach it from the gills. The entire intact heart was removed by pinching the bulbus arteriosus with a forceps and making one final cut between the atrium and sinus venosus. For RNA extractions hearts were rinsed in sterile PBS and stored in RNAlater® until use. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. T…	Experimental Factor: genotype:wild type genotype\|Experimental Factor: developmental stage:adult\|Experimental Factor: organism part:heart	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	NextSeq 500		ERP115040	NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls	ENA FIRST PUBLIC:2021 04 30\|ENA LAST UPDATE:2019 04 30	HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1WTheart1_1.fq.gz HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1WTheart1_2.fq.gz	fastq fastq	6814600800.0	42591255.0	E MTAB 7920:HJGMYBGX2 Zebrafish mRNA 17s001029 1 1 Morris lane1WTheart1	0:80 1:80	A:1823108307;C:1567497576;G:1587567005;T:1835589927;N:837985	80	80			1823108307	1567497576	1587567005	1835589927	837985	ERX3327068	ERS3389656	ERA1880314	Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway\|European Nucleotide Archive	Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway\|European Nucleotide Archive	2	0.93109	0.94806	0.07581	0.07635	0.75907	0.75988	0.54746	0.54753	80	80	B	B	biological fallback assumption	illumina	nextseq	3prime	poly_a	trueseq	bulk	bulk	bulk	Ireland	2019-04-30	Adult	Adult	Multi-tissue	Multi-system
9708	9708	ERR3300997	ERX3327064	ERS3389652	ERP115040	PRJEB32363	RNA seq of zebrafish sa12692 mutants against WT controls	E-MTAB-7920	Transcriptome Analysis	Arrhythmogenic Right Ventricular Cardiomyopathy is a congenital heart disorder characterized by fibrofatty replacement of the myocardium. The exact molecular mechanisms underlying the disease remain to be elucidated and treatment options are limited. The sa12692 mutant line contains a splice site mutation in the plakoglobin gene resulting in the expression of a truncated protein. This protein is highly similar to the protein expressed in Naxos disease a recessive form of ARVC. RNA seq was used to investigate the effect of the sa12692 mutation on gene expression in order to uncover signalling pathways involved in the pathogenesis of ARVC. Gene expression was examined in whole larvae at 5 dpf and in hearts of 1 year old adult fish. Larvae at 5 dpf were selected as this timepoint is equivalent to birth in humans. Adult hearts were selected as ARVC is a disorder of the heart and cardiac symptoms generally manifest in maturity. Hence the molecular effect of the mutation could be profiled at two life stages.	ENA FIRST PUBLIC:2021 04 30\|ENA LAST UPDATE:2019 04 30	Protocols: Each adult fish was euthanized using MS 222 and secured ventral side up in a Petri dish. A micro scissors was used to make an incision from the base of one pectoral fin to the other. A second incision was made from the centre of the first incision to the gill area. Fine needles were used to pin back the chest wall and expose the heart. The ventricle atrium and bulbus arteriosus were located. The bulbus arteriosus was cut to detach it from the gills. The entire intact heart was removed by pinching the bulbus arteriosus with a forceps and making one final cut between the atrium and sinus venosus. For RNA extractions hearts were rinsed in sterile PBS and stored in RNAlater® until use. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend th…	Mutant heart rep 3	SAMEA5585428	Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway	ENA FIRST PUBLIC:2021 04 30T00:25:03Z\|ENA LAST UPDATE:2019 04 30T15:21:46Z\|External Id:SAMEA5585428\|INSDC center name:Dept. of Pharmacology and Therapeutics College of Medicine Nursing and Heath Sciences National University of Ireland Galway\|INSDC first public:2021 04 30T00:25:03Z\|INSDC last update:2019 04 30T15:21:46Z\|INSDC status:public\|Submitter Id:E MTAB 7920:Mutant heart rep 3\|age:1\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|disease:Naxos disease\|genotype:sa12692 mutant\|individual:3\|organism part:heart\|sample name:E MTAB 7920:Mutant heart rep 3\|scientific name:Danio rerio\|sex:female\|strain:sa12692 mutant	NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls	E MTAB 7920:Mutant heart rep 3 p	Mutant heart rep 3 p	RNA seq of zebrafish sa12692 mutants against WT controls	Each adult fish was euthanized using MS 222 and secured ventral side up in a Petri dish. A micro scissors was used to make an incision from the base of one pectoral fin to the other. A second incision was made from the centre of the first incision to the gill area. Fine needles were used to pin back the chest wall and expose the heart. The ventricle atrium and bulbus arteriosus were located. The bulbus arteriosus was cut to detach it from the gills. The entire intact heart was removed by pinching the bulbus arteriosus with a forceps and making one final cut between the atrium and sinus venosus. For RNA extractions hearts were rinsed in sterile PBS and stored in RNAlater® until use. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. T…	Experimental Factor: genotype:sa12692 mutant\|Experimental Factor: developmental stage:adult\|Experimental Factor: organism part:heart	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	NextSeq 500		ERP115040	NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls	ENA FIRST PUBLIC:2021 04 30\|ENA LAST UPDATE:2019 04 30	HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1Mutantheart3_1.fq.gz HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1Mutantheart3_2.fq.gz	fastq fastq	7240447520.0	45252797.0	E MTAB 7920:HJGMYBGX2 Zebrafish mRNA 17s001029 1 1 Morris lane1Mutantheart3	0:80 1:80	A:1968283412;C:1645458614;G:1652590010;T:1973242527;N:872957	80	80			1968283412	1645458614	1652590010	1973242527	872957	ERX3327064	ERS3389652	ERA1880314	Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway\|European Nucleotide Archive	Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway\|European Nucleotide Archive	2	0.92784	0.94597	0.08601	0.08686	0.76702	0.76449	0.50929	0.52685	80	80	B	B	biological fallback assumption	illumina	nextseq	3prime	poly_a	trueseq	bulk	bulk	bulk	Ireland	2019-04-30	Adult	Adult	Multi-tissue	Multi-system
9709	9709	ERR3300996	ERX3327063	ERS3389651	ERP115040	PRJEB32363	RNA seq of zebrafish sa12692 mutants against WT controls	E-MTAB-7920	Transcriptome Analysis	Arrhythmogenic Right Ventricular Cardiomyopathy is a congenital heart disorder characterized by fibrofatty replacement of the myocardium. The exact molecular mechanisms underlying the disease remain to be elucidated and treatment options are limited. The sa12692 mutant line contains a splice site mutation in the plakoglobin gene resulting in the expression of a truncated protein. This protein is highly similar to the protein expressed in Naxos disease a recessive form of ARVC. RNA seq was used to investigate the effect of the sa12692 mutation on gene expression in order to uncover signalling pathways involved in the pathogenesis of ARVC. Gene expression was examined in whole larvae at 5 dpf and in hearts of 1 year old adult fish. Larvae at 5 dpf were selected as this timepoint is equivalent to birth in humans. Adult hearts were selected as ARVC is a disorder of the heart and cardiac symptoms generally manifest in maturity. Hence the molecular effect of the mutation could be profiled at two life stages.	ENA FIRST PUBLIC:2021 04 30\|ENA LAST UPDATE:2019 04 30	Protocols: Each adult fish was euthanized using MS 222 and secured ventral side up in a Petri dish. A micro scissors was used to make an incision from the base of one pectoral fin to the other. A second incision was made from the centre of the first incision to the gill area. Fine needles were used to pin back the chest wall and expose the heart. The ventricle atrium and bulbus arteriosus were located. The bulbus arteriosus was cut to detach it from the gills. The entire intact heart was removed by pinching the bulbus arteriosus with a forceps and making one final cut between the atrium and sinus venosus. For RNA extractions hearts were rinsed in sterile PBS and stored in RNAlater® until use. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend th…	Mutant heart rep 2	SAMEA5585427	Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway	ENA FIRST PUBLIC:2021 04 30T00:25:03Z\|ENA LAST UPDATE:2019 04 30T15:21:46Z\|External Id:SAMEA5585427\|INSDC center name:Dept. of Pharmacology and Therapeutics College of Medicine Nursing and Heath Sciences National University of Ireland Galway\|INSDC first public:2021 04 30T00:25:03Z\|INSDC last update:2019 04 30T15:21:46Z\|INSDC status:public\|Submitter Id:E MTAB 7920:Mutant heart rep 2\|age:1\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|disease:Naxos disease\|genotype:sa12692 mutant\|individual:2\|organism part:heart\|sample name:E MTAB 7920:Mutant heart rep 2\|scientific name:Danio rerio\|sex:female\|strain:sa12692 mutant	NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls	E MTAB 7920:Mutant heart rep 2 p	Mutant heart rep 2 p	RNA seq of zebrafish sa12692 mutants against WT controls	Each adult fish was euthanized using MS 222 and secured ventral side up in a Petri dish. A micro scissors was used to make an incision from the base of one pectoral fin to the other. A second incision was made from the centre of the first incision to the gill area. Fine needles were used to pin back the chest wall and expose the heart. The ventricle atrium and bulbus arteriosus were located. The bulbus arteriosus was cut to detach it from the gills. The entire intact heart was removed by pinching the bulbus arteriosus with a forceps and making one final cut between the atrium and sinus venosus. For RNA extractions hearts were rinsed in sterile PBS and stored in RNAlater® until use. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. T…	Experimental Factor: genotype:sa12692 mutant\|Experimental Factor: developmental stage:adult\|Experimental Factor: organism part:heart	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	NextSeq 500		ERP115040	NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls	ENA FIRST PUBLIC:2021 04 30\|ENA LAST UPDATE:2019 04 30	HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1Mutantheart2_1.fq.gz HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1Mutantheart2_2.fq.gz	fastq fastq	7347029600.0	45918935.0	E MTAB 7920:HJGMYBGX2 Zebrafish mRNA 17s001029 1 1 Morris lane1Mutantheart2	0:80 1:80	A:1967915665;C:1690507331;G:1712776156;T:1974918219;N:912229	80	80			1967915665	1690507331	1712776156	1974918219	912229	ERX3327063	ERS3389651	ERA1880314	Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway\|European Nucleotide Archive	Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway\|European Nucleotide Archive	2	0.93337	0.94978	0.07673	0.07724	0.76755	0.76798	0.53415	0.51157	80	80	B	B	biological fallback assumption	illumina	nextseq	3prime	poly_a	trueseq	bulk	bulk	bulk	Ireland	2019-04-30	Adult	Adult	Multi-tissue	Multi-system
9710	9710	ERR3300995	ERX3327062	ERS3389650	ERP115040	PRJEB32363	RNA seq of zebrafish sa12692 mutants against WT controls	E-MTAB-7920	Transcriptome Analysis	Arrhythmogenic Right Ventricular Cardiomyopathy is a congenital heart disorder characterized by fibrofatty replacement of the myocardium. The exact molecular mechanisms underlying the disease remain to be elucidated and treatment options are limited. The sa12692 mutant line contains a splice site mutation in the plakoglobin gene resulting in the expression of a truncated protein. This protein is highly similar to the protein expressed in Naxos disease a recessive form of ARVC. RNA seq was used to investigate the effect of the sa12692 mutation on gene expression in order to uncover signalling pathways involved in the pathogenesis of ARVC. Gene expression was examined in whole larvae at 5 dpf and in hearts of 1 year old adult fish. Larvae at 5 dpf were selected as this timepoint is equivalent to birth in humans. Adult hearts were selected as ARVC is a disorder of the heart and cardiac symptoms generally manifest in maturity. Hence the molecular effect of the mutation could be profiled at two life stages.	ENA FIRST PUBLIC:2021 04 30\|ENA LAST UPDATE:2019 04 30	Protocols: Each adult fish was euthanized using MS 222 and secured ventral side up in a Petri dish. A micro scissors was used to make an incision from the base of one pectoral fin to the other. A second incision was made from the centre of the first incision to the gill area. Fine needles were used to pin back the chest wall and expose the heart. The ventricle atrium and bulbus arteriosus were located. The bulbus arteriosus was cut to detach it from the gills. The entire intact heart was removed by pinching the bulbus arteriosus with a forceps and making one final cut between the atrium and sinus venosus. For RNA extractions hearts were rinsed in sterile PBS and stored in RNAlater® until use. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend th…	Mutant heart rep 1	SAMEA5585426	Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway	ENA FIRST PUBLIC:2021 04 30T00:25:02Z\|ENA LAST UPDATE:2019 04 30T15:21:46Z\|External Id:SAMEA5585426\|INSDC center name:Dept. of Pharmacology and Therapeutics College of Medicine Nursing and Heath Sciences National University of Ireland Galway\|INSDC first public:2021 04 30T00:25:02Z\|INSDC last update:2019 04 30T15:21:46Z\|INSDC status:public\|Submitter Id:E MTAB 7920:Mutant heart rep 1\|age:1\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|disease:Naxos disease\|genotype:sa12692 mutant\|individual:1\|organism part:heart\|sample name:E MTAB 7920:Mutant heart rep 1\|scientific name:Danio rerio\|sex:female\|strain:sa12692 mutant	NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls	E MTAB 7920:Mutant heart rep 1 p	Mutant heart rep 1 p	RNA seq of zebrafish sa12692 mutants against WT controls	Each adult fish was euthanized using MS 222 and secured ventral side up in a Petri dish. A micro scissors was used to make an incision from the base of one pectoral fin to the other. A second incision was made from the centre of the first incision to the gill area. Fine needles were used to pin back the chest wall and expose the heart. The ventricle atrium and bulbus arteriosus were located. The bulbus arteriosus was cut to detach it from the gills. The entire intact heart was removed by pinching the bulbus arteriosus with a forceps and making one final cut between the atrium and sinus venosus. For RNA extractions hearts were rinsed in sterile PBS and stored in RNAlater® until use. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. T…	Experimental Factor: genotype:sa12692 mutant\|Experimental Factor: developmental stage:adult\|Experimental Factor: organism part:heart	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	NextSeq 500		ERP115040	NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls	ENA FIRST PUBLIC:2021 04 30\|ENA LAST UPDATE:2019 04 30	HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1Mutantheart1_1.fq.gz HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1Mutantheart1_2.fq.gz	fastq fastq	6296502880.0	39353143.0	E MTAB 7920:HJGMYBGX2 Zebrafish mRNA 17s001029 1 1 Morris lane1Mutantheart1	0:80 1:80	A:1677737687;C:1460767489;G:1468915029;T:1688319734;N:762941	80	80			1677737687	1460767489	1468915029	1688319734	762941	ERX3327062	ERS3389650	ERA1880314	Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway\|European Nucleotide Archive	Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway\|European Nucleotide Archive	2	0.93775	0.9516	0.07994	0.08077	0.75844	0.75759	0.51937	0.52207	80	80	B	B	biological fallback assumption	illumina	nextseq	3prime	poly_a	trueseq	bulk	bulk	bulk	Ireland	2019-04-30	Adult	Adult	Multi-tissue	Multi-system
10149	10149	ERR5005145	ERX4814428	ERS5474665	ERP125923	PRJEB42059	RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain	E-MTAB-9924	Other	DNA methylation predominantly occurs at CG dinucleotides in vertebrate genomes however non CG methylation mCH is also detectable in vertebrate tissues most notably in the nervous system. In mammalian brains it is well established that: i mCH is targeted to CAC trinucleotides by DNMT3A ii enriched in gene bodies and repetitive elements and iii associated with transcriptional repression. However the possible conservation of these mCH features in zebrafish is largely unexplored and has yet to be functionally demonstrated. In this study we analyse the transcriptomes RNA seq and methylome RRBS of developing zebrafish larvae 1 6 weeks and adult brain 6 month. We additionally elucidate a role for dnmt3aa/dnmt3ab in mCH deposition via CRISP/CAS9 KO and WGBS of 4 wpf brains	ENA FIRST PUBLIC:2020 12 18\|ENA LAST UPDATE:2020 12 17	Protocols: Whole brains were dissected from zebrafish larvae and adults before being snap frozen in liquid nitrogen and stored at 80°C Genomic DNA gDNA was extracted from brains using the QIAGEN DNeasy Blood & Tissue Kit QIAGEN Chadstone VIC Australia according to manufacturer instructions. For RNA extraction half the lysate from the first step of the DNA extraction from the QIAGEN DNeasy Blood & Tissue Kit was added to TRIsure Bioline and purified following manufacturer instructions. All experiments in this study were performed in biological replicates. RNA seq libraries were prepared with 1000ng of input RNA material using the KAPA mRNA HyperPrep Kit according to the manufacturer's instructions.	adult rep2 RNA	SAMEA7727292	Genomics and Epigenetics Division, Garvan Institute of Medical Research,	ENA first public:2020 12 18\|ENA last update:2020 12 17\|External Id:SAMEA7727292\|INSDC center alias:Genomics and Epigenetics Division Garvan Institute of Medical Research \|INSDC center name:Genomics and Epigenetics Division Garvan Institute of Medical Research \|INSDC first public:2020 12 18T17:06:48Z\|INSDC last update:2020 12 17T08:36:39Z\|INSDC status:public\|Submitter Id:E MTAB 9924:adult rep2 RNA\|age:6\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:wild type genotype\|individual:5\|organism part:brain\|sample name:E MTAB 9924:adult rep2 RNA\|sex:mixed\|strain:Mixed AB and Tubingen	HiSeq X Ten paired end sequencing; RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain	E MTAB 9924:adult rep2 RNA p	adult rep2 RNA p	RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain	Whole brains were dissected from zebrafish larvae and adults before being snap frozen in liquid nitrogen and stored at 80°C Genomic DNA gDNA was extracted from brains using the QIAGEN DNeasy Blood & Tissue Kit QIAGEN Chadstone VIC Australia according to manufacturer instructions. For RNA extraction half the lysate from the first step of the DNA extraction from the QIAGEN DNeasy Blood & Tissue Kit was added to TRIsure Bioline and purified following manufacturer instructions. All experiments in this study were performed in biological replicates. RNA seq libraries were prepared with 1000ng of input RNA material using the KAPA mRNA HyperPrep Kit according to the manufacturer's instructions.	Experimental Factor: age:6\|Experimental Factor: genotype:wild type genotype\|Experimental Factor: protocol:RNA Seq	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	HiSeq X Ten		ERP125923	HiSeq X Ten paired end sequencing; RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain	ENA FIRST PUBLIC:2020 12 18\|ENA LAST UPDATE:2020 12 17	adult_rep2_RNA_R1.fastq.gz adult_rep2_RNA_R2.fastq.gz	fastq fastq	15648506033.0	52770962.0	E MTAB 9924:adult rep2 RNA R	0:148.45 1:148.09	A:4268818428;C:3540462921;G:3548332979;T:4288409679;N:2482026	148	148			4268818428	3540462921	3548332979	4288409679	2482026	ERX4814428	ERS5474665	ERA3199751	Genomics and Epigenetics Division, Garvan Institute of Medical Research,\|European Nucleotide Archive	Genomics and Epigenetics Division, Garvan Institute of Medical Research,\|European Nucleotide Archive	2	0.94625	0.94771	0.13596	0.1321	0.691	0.70709	0.53016	0.5357	148	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Australia	2020-12-17	Adult	Adult	Multi-tissue	Multi-system
10150	10150	ERR5005144	ERX4814427	ERS5474664	ERP125923	PRJEB42059	RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain	E-MTAB-9924	Other	DNA methylation predominantly occurs at CG dinucleotides in vertebrate genomes however non CG methylation mCH is also detectable in vertebrate tissues most notably in the nervous system. In mammalian brains it is well established that: i mCH is targeted to CAC trinucleotides by DNMT3A ii enriched in gene bodies and repetitive elements and iii associated with transcriptional repression. However the possible conservation of these mCH features in zebrafish is largely unexplored and has yet to be functionally demonstrated. In this study we analyse the transcriptomes RNA seq and methylome RRBS of developing zebrafish larvae 1 6 weeks and adult brain 6 month. We additionally elucidate a role for dnmt3aa/dnmt3ab in mCH deposition via CRISP/CAS9 KO and WGBS of 4 wpf brains	ENA FIRST PUBLIC:2020 12 18\|ENA LAST UPDATE:2020 12 17	Protocols: Whole brains were dissected from zebrafish larvae and adults before being snap frozen in liquid nitrogen and stored at 80°C Genomic DNA gDNA was extracted from brains using the QIAGEN DNeasy Blood & Tissue Kit QIAGEN Chadstone VIC Australia according to manufacturer instructions. For RNA extraction half the lysate from the first step of the DNA extraction from the QIAGEN DNeasy Blood & Tissue Kit was added to TRIsure Bioline and purified following manufacturer instructions. All experiments in this study were performed in biological replicates. RNA seq libraries were prepared with 1000ng of input RNA material using the KAPA mRNA HyperPrep Kit according to the manufacturer's instructions.	adult rep1 RNA	SAMEA7727291	Genomics and Epigenetics Division, Garvan Institute of Medical Research,	ENA first public:2020 12 18\|ENA last update:2020 12 17\|External Id:SAMEA7727291\|INSDC center alias:Genomics and Epigenetics Division Garvan Institute of Medical Research \|INSDC center name:Genomics and Epigenetics Division Garvan Institute of Medical Research \|INSDC first public:2020 12 18T17:06:48Z\|INSDC last update:2020 12 17T08:36:39Z\|INSDC status:public\|Submitter Id:E MTAB 9924:adult rep1 RNA\|age:6\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:wild type genotype\|individual:5\|organism part:brain\|sample name:E MTAB 9924:adult rep1 RNA\|sex:mixed\|strain:Mixed AB and Tubingen	HiSeq X Ten paired end sequencing; RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain	E MTAB 9924:adult rep1 RNA p	adult rep1 RNA p	RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain	Whole brains were dissected from zebrafish larvae and adults before being snap frozen in liquid nitrogen and stored at 80°C Genomic DNA gDNA was extracted from brains using the QIAGEN DNeasy Blood & Tissue Kit QIAGEN Chadstone VIC Australia according to manufacturer instructions. For RNA extraction half the lysate from the first step of the DNA extraction from the QIAGEN DNeasy Blood & Tissue Kit was added to TRIsure Bioline and purified following manufacturer instructions. All experiments in this study were performed in biological replicates. RNA seq libraries were prepared with 1000ng of input RNA material using the KAPA mRNA HyperPrep Kit according to the manufacturer's instructions.	Experimental Factor: age:6\|Experimental Factor: genotype:wild type genotype\|Experimental Factor: protocol:RNA Seq	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	HiSeq X Ten		ERP125923	HiSeq X Ten paired end sequencing; RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain	ENA FIRST PUBLIC:2020 12 18\|ENA LAST UPDATE:2020 12 17	adult_rep1_RNA_R1.fastq.gz adult_rep1_RNA_R2.fastq.gz	fastq fastq	12526662412.0	42363955.0	E MTAB 9924:adult rep1 RNA R	0:148.02 1:147.67	A:3489175783;C:2756879350;G:2771544913;T:3507538808;N:1523558	148	147			3489175783	2756879350	2771544913	3507538808	1523558	ERX4814427	ERS5474664	ERA3199751	Genomics and Epigenetics Division, Garvan Institute of Medical Research,\|European Nucleotide Archive	Genomics and Epigenetics Division, Garvan Institute of Medical Research,\|European Nucleotide Archive	2	0.94246	0.94448	0.14788	0.14431	0.70065	0.7181	0.50361	0.50894	149	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Australia	2020-12-17	Adult	Adult	Multi-tissue	Multi-system
10166	10166	ERR5762357	ERX5471113	ERS6291553	ERP128548	PRJEB44492	scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish	E-MTAB-10370	Transcriptome Analysis	GATA2 is a pivotal hematopoietic transcription factor required for generation and maintenance of hematopoietic stem cells HSCs. Due to early embryonic lethality of Gata2 deficiency in mice its role during adult hematopoiesis is incompletely understood. In zebrafish mammalian functions of Gata2 are split between two orthologues: Gata2a and Gata2b. Previous studies have shown that Gata2b is prominently expressed in hematopoietic stem and progenitor cells HSPCs whereas Gata2a is mainly expressed in the vasculature. We found that Gata2b deficient zebrafish have a reduction in embryonic definitive HSPC numbers and have impaired myeloid lineage differentiation but are viable. This allowed us to study the role of Gata2b in adult hematopoiesis. To assess the impact of Gata2b deficiency on the transcriptional profile of HSPCs and differentiated cells we sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and germline Gata2b deficient zebrafish based on scatter profiles and processed for single cell RNA sequencing. To enrich the scarce HSC population we used pooled KM from two WT and Gata2b deficient TgCD41:GFP zebrafish per sample and included all CD41:GFPlow expressing cells present in the kidney marrow pool as these cells were shown to contain transplantable HSCs.	ENA FIRST PUBLIC:2022 04 09\|ENA LAST UPDATE:2022 04 09	Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V2. Library was prepared using the manufacturers protocol 10x Chromium V2.	wt2 gata2b	SAMEA8606934	Erasmus Medical Center	ENA FIRST PUBLIC:2022 04 09\|ENA LAST UPDATE:2022 04 09\|External Id:SAMEA8606934\|INSDC center alias:Erasmus Medical Center\|INSDC center name:Erasmus Medical Center\|INSDC first public:2022 04 09T00:20:19Z\|INSDC last update:2022 04 09T00:20:19Z\|INSDC status:public\|Submitter Id:E MTAB 10370:wt2 gata2b\|age:5\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:wild type genotype\|isolate:not applicable\|organism part:kidney\|sample name:E MTAB 10370:wt2 gata2b\|sampling site:kidney marrow\|sex:female\|strain:AB	Illumina NovaSeq 6000 paired end sequencing; scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish	E MTAB 10370:wt2 gata2b p	wt2 gata2b p	scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish	Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V2. Library was prepared using the manufacturers protocol 10x Chromium V2.	Experimental Factor: genotype:wild type genotype	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP128548	Illumina NovaSeq 6000 paired end sequencing; scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish	ENA FIRST PUBLIC:2022 04 09\|ENA LAST UPDATE:2022 04 09	wt2_gata2b.bam	bam	25266437196.0	277653156.0	E MTAB 10370:wt2 gata2b	0:91	A:7555470312;C:5144518052;G:5682746714;T:6882396490;N:1305628	91				7555470312	5144518052	5682746714	6882396490	1305628	ERX5471113	ERS6291553	ERA4089475	Erasmus Medical Center\|European Nucleotide Archive	Erasmus Medical Center\|European Nucleotide Archive	1	0.90876		0.18424		0.84017		0.55508		91		B		usable mapping rate	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Netherlands	2022-04-09	Adult	Adult	Kidney	Renal System
10167	10167	ERR5762356	ERX5471112	ERS6291552	ERP128548	PRJEB44492	scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish	E-MTAB-10370	Transcriptome Analysis	GATA2 is a pivotal hematopoietic transcription factor required for generation and maintenance of hematopoietic stem cells HSCs. Due to early embryonic lethality of Gata2 deficiency in mice its role during adult hematopoiesis is incompletely understood. In zebrafish mammalian functions of Gata2 are split between two orthologues: Gata2a and Gata2b. Previous studies have shown that Gata2b is prominently expressed in hematopoietic stem and progenitor cells HSPCs whereas Gata2a is mainly expressed in the vasculature. We found that Gata2b deficient zebrafish have a reduction in embryonic definitive HSPC numbers and have impaired myeloid lineage differentiation but are viable. This allowed us to study the role of Gata2b in adult hematopoiesis. To assess the impact of Gata2b deficiency on the transcriptional profile of HSPCs and differentiated cells we sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and germline Gata2b deficient zebrafish based on scatter profiles and processed for single cell RNA sequencing. To enrich the scarce HSC population we used pooled KM from two WT and Gata2b deficient TgCD41:GFP zebrafish per sample and included all CD41:GFPlow expressing cells present in the kidney marrow pool as these cells were shown to contain transplantable HSCs.	ENA FIRST PUBLIC:2022 04 09\|ENA LAST UPDATE:2022 04 09	Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V2. Library was prepared using the manufacturers protocol 10x Chromium V2.	wt1 gata2b	SAMEA8606933	Erasmus Medical Center	ENA FIRST PUBLIC:2022 04 09\|ENA LAST UPDATE:2022 04 09\|External Id:SAMEA8606933\|INSDC center alias:Erasmus Medical Center\|INSDC center name:Erasmus Medical Center\|INSDC first public:2022 04 09T00:20:19Z\|INSDC last update:2022 04 09T00:20:19Z\|INSDC status:public\|Submitter Id:E MTAB 10370:wt1 gata2b\|age:5\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:wild type genotype\|isolate:not applicable\|organism part:kidney\|sample name:E MTAB 10370:wt1 gata2b\|sampling site:kidney marrow\|sex:female\|strain:AB	Illumina NovaSeq 6000 paired end sequencing; scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish	E MTAB 10370:wt1 gata2b p	wt1 gata2b p	scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish	Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V2. Library was prepared using the manufacturers protocol 10x Chromium V2.	Experimental Factor: genotype:wild type genotype	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP128548	Illumina NovaSeq 6000 paired end sequencing; scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish	ENA FIRST PUBLIC:2022 04 09\|ENA LAST UPDATE:2022 04 09	wt1_gata2b.bam	bam	36376708095.0	399744045.0	E MTAB 10370:wt1 gata2b	0:91	A:10397161431;C:8128518427;G:8799445454;T:9049686061;N:1896722	91				10397161431	8128518427	8799445454	9049686061	1896722	ERX5471112	ERS6291552	ERA4089475	Erasmus Medical Center\|European Nucleotide Archive	Erasmus Medical Center\|European Nucleotide Archive	1	0.94708		0.08938		0.85449		0.52917		91		B		usable mapping rate	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Netherlands	2022-04-09	Adult	Adult	Kidney	Renal System
10168	10168	ERR5762355	ERX5471111	ERS6291551	ERP128548	PRJEB44492	scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish	E-MTAB-10370	Transcriptome Analysis	GATA2 is a pivotal hematopoietic transcription factor required for generation and maintenance of hematopoietic stem cells HSCs. Due to early embryonic lethality of Gata2 deficiency in mice its role during adult hematopoiesis is incompletely understood. In zebrafish mammalian functions of Gata2 are split between two orthologues: Gata2a and Gata2b. Previous studies have shown that Gata2b is prominently expressed in hematopoietic stem and progenitor cells HSPCs whereas Gata2a is mainly expressed in the vasculature. We found that Gata2b deficient zebrafish have a reduction in embryonic definitive HSPC numbers and have impaired myeloid lineage differentiation but are viable. This allowed us to study the role of Gata2b in adult hematopoiesis. To assess the impact of Gata2b deficiency on the transcriptional profile of HSPCs and differentiated cells we sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and germline Gata2b deficient zebrafish based on scatter profiles and processed for single cell RNA sequencing. To enrich the scarce HSC population we used pooled KM from two WT and Gata2b deficient TgCD41:GFP zebrafish per sample and included all CD41:GFPlow expressing cells present in the kidney marrow pool as these cells were shown to contain transplantable HSCs.	ENA FIRST PUBLIC:2022 04 09\|ENA LAST UPDATE:2022 04 09	Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V2. Library was prepared using the manufacturers protocol 10x Chromium V2.	hom2 gata2b	SAMEA8606932	Erasmus Medical Center	ENA FIRST PUBLIC:2022 04 09\|ENA LAST UPDATE:2022 04 09\|External Id:SAMEA8606932\|INSDC center alias:Erasmus Medical Center\|INSDC center name:Erasmus Medical Center\|INSDC first public:2022 04 09T00:20:19Z\|INSDC last update:2022 04 09T00:20:19Z\|INSDC status:public\|Submitter Id:E MTAB 10370:hom2 gata2b\|age:5\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:gata2b / \|isolate:not applicable\|organism part:kidney\|sample name:E MTAB 10370:hom2 gata2b\|sampling site:kidney marrow\|sex:female\|strain:AB	Illumina NovaSeq 6000 paired end sequencing; scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish	E MTAB 10370:hom2 gata2b p	hom2 gata2b p	scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish	Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V2. Library was prepared using the manufacturers protocol 10x Chromium V2.	Experimental Factor: genotype:gata2b /	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP128548	Illumina NovaSeq 6000 paired end sequencing; scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish	ENA FIRST PUBLIC:2022 04 09\|ENA LAST UPDATE:2022 04 09	hom2_gata2b.bam	bam	22416887402.0	246339422.0	E MTAB 10370:hom2 gata2b	0:91	A:6732382430;C:4540586585;G:4933684272;T:6209137814;N:1096301	91				6732382430	4540586585	4933684272	6209137814	1096301	ERX5471111	ERS6291551	ERA4089475	Erasmus Medical Center\|European Nucleotide Archive	Erasmus Medical Center\|European Nucleotide Archive	1	0.91306		0.21566		0.83469		0.53782		91		B		usable mapping rate	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Netherlands	2022-04-09	Adult	Adult	Kidney	Renal System
10169	10169	ERR5762354	ERX5471110	ERS6291550	ERP128548	PRJEB44492	scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish	E-MTAB-10370	Transcriptome Analysis	GATA2 is a pivotal hematopoietic transcription factor required for generation and maintenance of hematopoietic stem cells HSCs. Due to early embryonic lethality of Gata2 deficiency in mice its role during adult hematopoiesis is incompletely understood. In zebrafish mammalian functions of Gata2 are split between two orthologues: Gata2a and Gata2b. Previous studies have shown that Gata2b is prominently expressed in hematopoietic stem and progenitor cells HSPCs whereas Gata2a is mainly expressed in the vasculature. We found that Gata2b deficient zebrafish have a reduction in embryonic definitive HSPC numbers and have impaired myeloid lineage differentiation but are viable. This allowed us to study the role of Gata2b in adult hematopoiesis. To assess the impact of Gata2b deficiency on the transcriptional profile of HSPCs and differentiated cells we sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and germline Gata2b deficient zebrafish based on scatter profiles and processed for single cell RNA sequencing. To enrich the scarce HSC population we used pooled KM from two WT and Gata2b deficient TgCD41:GFP zebrafish per sample and included all CD41:GFPlow expressing cells present in the kidney marrow pool as these cells were shown to contain transplantable HSCs.	ENA FIRST PUBLIC:2022 04 09\|ENA LAST UPDATE:2022 04 09	Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V2. Library was prepared using the manufacturers protocol 10x Chromium V2.	hom1 gata2b	SAMEA8606931	Erasmus Medical Center	ENA FIRST PUBLIC:2022 04 09\|ENA LAST UPDATE:2022 04 09\|External Id:SAMEA8606931\|INSDC center alias:Erasmus Medical Center\|INSDC center name:Erasmus Medical Center\|INSDC first public:2022 04 09T00:20:19Z\|INSDC last update:2022 04 09T00:20:19Z\|INSDC status:public\|Submitter Id:E MTAB 10370:hom1 gata2b\|age:5\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:gata2b / \|isolate:not applicable\|organism part:kidney\|sample name:E MTAB 10370:hom1 gata2b\|sampling site:kidney marrow\|sex:female\|strain:AB	Illumina NovaSeq 6000 paired end sequencing; scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish	E MTAB 10370:hom1 gata2b p	hom1 gata2b p	scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish	Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V2. Library was prepared using the manufacturers protocol 10x Chromium V2.	Experimental Factor: genotype:gata2b /	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP128548	Illumina NovaSeq 6000 paired end sequencing; scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish	ENA FIRST PUBLIC:2022 04 09\|ENA LAST UPDATE:2022 04 09	hom1_gata2b.bam	bam	18004290759.0	197849349.0	E MTAB 10370:hom1 gata2b	0:91	A:5232521408;C:3876317502;G:4287902596;T:4606191653;N:1357600	91				5232521408	3876317502	4287902596	4606191653	1357600	ERX5471110	ERS6291550	ERA4089475	Erasmus Medical Center\|European Nucleotide Archive	Erasmus Medical Center\|European Nucleotide Archive	1	0.94131		0.08871		0.83465		0.52792		91		B		usable mapping rate	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Netherlands	2022-04-09	Adult	Adult	Kidney	Renal System
11017	11017	ERR9750937	ERX9298876	ERS12023662	ERP137743	PRJEB52989	scRNAseq of post amputation regenerating zebrafish cardiac ventricle	E-MTAB-10643	Transcriptome Analysis	Adult zebrafish hearts have the ability to regenerate. The roles of non myocytes in this process have remained elusive. Here we have performed 2 scRNAseq experiments on interstitial cells. Experiment 1 E1 included interstitial cells obtained from uninjured regenerating 3 days 7 days and 14 days post apical amputation. Experiment 2 E2 included cells from uninjured sham operated abdomen opened and regenerating 3 dy post amputation with and without xxx inhibitor NSC40520 treatment. Cells were obtained by heart dissection followed by enzymatic dissociation and FACS sorting of single viable nucleated cells.	ENA FIRST PUBLIC:2022 05 20\|ENA LAST UPDATE:2022 05 20	Protocols: Zebrafish were euthanized in tricaine and hearts were extracted in PBS Hearts were pooled and pre digested for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this tissue was gently dissociated and passed through a cell strainer 40um spun down 5min 300g and resuspended in HBSS 2% fetal calf serum. The heart was exposed and approximately 20% of the ventricle removed Zebrafish were treated with MMP inhibitor NSC405020 for three days following surgery. Amplified cDNA was used for three prime RNA seq library generation RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.	Expt 2 Uninjured	SAMEA14418104	IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.	ENA first public:2022 05 20\|ENA last update:2022 05 20\|External Id:SAMEA14418104\|INSDC center alias:IGF CNRS INSERM Univ. Montpellier LabEx ICST F 34094 Montpellier France.\|INSDC center name:IGF CNRS INSERM Univ. Montpellier LabEx ICST F 34094 Montpellier France.\|INSDC first public:2022 05 20T16:17:49Z\|INSDC last update:2022 05 20T16:17:49Z\|INSDC status:public\|Submitter Id:E MTAB 10643:Expt 2 Uninjured\|age:6\|broker name:ArrayExpress\|cell type:interstitial cell\|common name:zebrafish\|developmental stage:adult\|genotype:wild type genotype\|organism part:heart\|sample name:E MTAB 10643:Expt 2 Uninjured\|sex:male\|strain:AB	Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle	E MTAB 10643:Expt 2 Uninjured p	Expt 2 Uninjured p	scRNAseq of post amputation regenerating zebrafish cardiac ventricle	Zebrafish were euthanized in tricaine and hearts were extracted in PBS "Hearts were pooled and ""pre digested"" for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this tissue was gently dissociated and passed through a cell strainer 40um spun down 5min 300g and resuspended in HBSS 2% fetal calf serum." The heart was exposed and approximately 20% of the ventricle removed Zebrafish were treated with MMP inhibitor NSC405020 for three days following surgery. Amplified cDNA was used for three prime RNA seq library generation RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.	Experimental Factor: injury:n1\|Experimental Factor: treatment:n1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	SINGLE	ILLUMINA	Illumina NovaSeq 6000		ERP137743	Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle	ENA FIRST PUBLIC:2022 05 20\|ENA LAST UPDATE:2022 05 20	E2_Uninjured_S2_L002_I1_001.fastq.gz E2_Uninjured_S2_L002_I2_001.fastq.gz E2_Uninjured_S2_L002_R1_001.fastq.gz E2_Uninjured_S2_L002_R2_001.fastq.gz	fastq fastq fastq fastq	9325673775.0	69079065.0	E MTAB 10643:Expt 2 Uninjured	0:10 1:10 2:28 3:87	A:1619571910;C:1420805235;G:1471531128;T:1496998088;N:972294	10	10	28	87	1619571910	1420805235	1471531128	1496998088	972294	ERX9298876	ERS12023662	ERA14538536	IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.\|European Nucleotide Archive	IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.\|European Nucleotide Archive	1	0.93798		0.11364		0.84843		0.53531		87		B		usable mapping rate	illumina	novaseq_era	3prime	poly_a	unknown	sc	single_cell_droplet	10x	France	2022-05-20	Adult	Adult	Heart	Cardiovascular System
11018	11018	ERR9750936	ERX9298875	ERS12023661	ERP137743	PRJEB52989	scRNAseq of post amputation regenerating zebrafish cardiac ventricle	E-MTAB-10643	Transcriptome Analysis	Adult zebrafish hearts have the ability to regenerate. The roles of non myocytes in this process have remained elusive. Here we have performed 2 scRNAseq experiments on interstitial cells. Experiment 1 E1 included interstitial cells obtained from uninjured regenerating 3 days 7 days and 14 days post apical amputation. Experiment 2 E2 included cells from uninjured sham operated abdomen opened and regenerating 3 dy post amputation with and without xxx inhibitor NSC40520 treatment. Cells were obtained by heart dissection followed by enzymatic dissociation and FACS sorting of single viable nucleated cells.	ENA FIRST PUBLIC:2022 05 20\|ENA LAST UPDATE:2022 05 20	Protocols: Zebrafish were euthanized in tricaine and hearts were extracted in PBS Hearts were pooled and pre digested for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this tissue was gently dissociated and passed through a cell strainer 40um spun down 5min 300g and resuspended in HBSS 2% fetal calf serum. The heart was exposed and approximately 20% of the ventricle removed Zebrafish were treated with MMP inhibitor NSC405020 for three days following surgery. Amplified cDNA was used for three prime RNA seq library generation RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.	Expt 2 Sham	SAMEA14418103	IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.	ENA first public:2022 05 20\|ENA last update:2022 05 20\|External Id:SAMEA14418103\|INSDC center alias:IGF CNRS INSERM Univ. Montpellier LabEx ICST F 34094 Montpellier France.\|INSDC center name:IGF CNRS INSERM Univ. Montpellier LabEx ICST F 34094 Montpellier France.\|INSDC first public:2022 05 20T16:17:49Z\|INSDC last update:2022 05 20T16:17:49Z\|INSDC status:public\|Submitter Id:E MTAB 10643:Expt 2 Sham\|age:6\|broker name:ArrayExpress\|cell type:interstitial cell\|common name:zebrafish\|developmental stage:adult\|genotype:wild type genotype\|injury:sham surgery\|organism part:heart\|sample name:E MTAB 10643:Expt 2 Sham\|sex:male\|strain:AB	Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle	E MTAB 10643:Expt 2 Sham p	Expt 2 Sham p	scRNAseq of post amputation regenerating zebrafish cardiac ventricle	Zebrafish were euthanized in tricaine and hearts were extracted in PBS "Hearts were pooled and ""pre digested"" for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this tissue was gently dissociated and passed through a cell strainer 40um spun down 5min 300g and resuspended in HBSS 2% fetal calf serum." The heart was exposed and approximately 20% of the ventricle removed Zebrafish were treated with MMP inhibitor NSC405020 for three days following surgery. Amplified cDNA was used for three prime RNA seq library generation RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.	Experimental Factor: injury:sham surgery\|Experimental Factor: time:3\|Experimental Factor: treatment:n1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	SINGLE	ILLUMINA	Illumina NovaSeq 6000		ERP137743	Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle	ENA FIRST PUBLIC:2022 05 20\|ENA LAST UPDATE:2022 05 20	E2_Sham_S1_L002_I1_001.fastq.gz E2_Sham_S1_L002_I2_001.fastq.gz E2_Sham_S1_L002_R1_001.fastq.gz E2_Sham_S1_L002_R2_001.fastq.gz	fastq fastq fastq fastq	11328674040.0	83916104.0	E MTAB 10643:Expt 2 Sham	0:10 1:10 2:28 3:87	A:1955327720;C:1746332187;G:1777122701;T:1820705338;N:1213102	10	10	28	87	1955327720	1746332187	1777122701	1820705338	1213102	ERX9298875	ERS12023661	ERA14538536	IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.\|European Nucleotide Archive	IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.\|European Nucleotide Archive	1	0.92847		0.09981		0.85707		0.46947		87		B		usable mapping rate	illumina	novaseq_era	3prime	poly_a	unknown	sc	single_cell_droplet	10x	France	2022-05-20	Adult	Adult	Heart	Cardiovascular System
11019	11019	ERR9750935	ERX9298874	ERS12023660	ERP137743	PRJEB52989	scRNAseq of post amputation regenerating zebrafish cardiac ventricle	E-MTAB-10643	Transcriptome Analysis	Adult zebrafish hearts have the ability to regenerate. The roles of non myocytes in this process have remained elusive. Here we have performed 2 scRNAseq experiments on interstitial cells. Experiment 1 E1 included interstitial cells obtained from uninjured regenerating 3 days 7 days and 14 days post apical amputation. Experiment 2 E2 included cells from uninjured sham operated abdomen opened and regenerating 3 dy post amputation with and without xxx inhibitor NSC40520 treatment. Cells were obtained by heart dissection followed by enzymatic dissociation and FACS sorting of single viable nucleated cells.	ENA FIRST PUBLIC:2022 05 20\|ENA LAST UPDATE:2022 05 20	Protocols: Zebrafish were euthanized in tricaine and hearts were extracted in PBS Hearts were pooled and pre digested for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this tissue was gently dissociated and passed through a cell strainer 40um spun down 5min 300g and resuspended in HBSS 2% fetal calf serum. The heart was exposed and approximately 20% of the ventricle removed Zebrafish were treated with MMP inhibitor NSC405020 for three days following surgery. Amplified cDNA was used for three prime RNA seq library generation RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.	Expt 2 3d post amputation	SAMEA14418102	IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.	ENA first public:2022 05 20\|ENA last update:2022 05 20\|External Id:SAMEA14418102\|INSDC center alias:IGF CNRS INSERM Univ. Montpellier LabEx ICST F 34094 Montpellier France.\|INSDC center name:IGF CNRS INSERM Univ. Montpellier LabEx ICST F 34094 Montpellier France.\|INSDC first public:2022 05 20T16:17:49Z\|INSDC last update:2022 05 20T16:17:49Z\|INSDC status:public\|Submitter Id:E MTAB 10643:Expt 2 3d post amputation\|age:6\|broker name:ArrayExpress\|cell type:interstitial cell\|common name:zebrafish\|developmental stage:adult\|genotype:wild type genotype\|injury:20 percent removal of the cardiac ventricle apex\|organism part:heart\|sample name:E MTAB 10643:Expt 2 3d post amputation\|sex:male\|strain:AB	Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle	E MTAB 10643:Expt 2 3d post amputation p	Expt 2 3d post amputation p	scRNAseq of post amputation regenerating zebrafish cardiac ventricle	Zebrafish were euthanized in tricaine and hearts were extracted in PBS "Hearts were pooled and ""pre digested"" for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this tissue was gently dissociated and passed through a cell strainer 40um spun down 5min 300g and resuspended in HBSS 2% fetal calf serum." The heart was exposed and approximately 20% of the ventricle removed Zebrafish were treated with MMP inhibitor NSC405020 for three days following surgery. Amplified cDNA was used for three prime RNA seq library generation RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.	Experimental Factor: injury:20 percent removal of the cardiac ventricle apex\|Experimental Factor: time:3\|Experimental Factor: treatment:n1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	SINGLE	ILLUMINA	Illumina NovaSeq 6000		ERP137743	Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle	ENA FIRST PUBLIC:2022 05 20\|ENA LAST UPDATE:2022 05 20	E2_3dpa_S3_L002_I1_001.fastq.gz E2_3dpa_S3_L002_I2_001.fastq.gz E2_3dpa_S3_L002_R1_001.fastq.gz E2_3dpa_S3_L002_R2_001.fastq.gz	fastq fastq fastq fastq	16111486440.0	119344344.0	E MTAB 10643:Expt 2 3d post amputation	0:10 1:10 2:28 3:87	A:2610144058;C:2617445332;G:2496763759;T:2656876552;N:1728227	10	10	28	87	2610144058	2617445332	2496763759	2656876552	1728227	ERX9298874	ERS12023660	ERA14538536	IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.\|European Nucleotide Archive	IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.\|European Nucleotide Archive	1	0.94868		0.07071		0.89221		0.54333		87		B		usable mapping rate	illumina	novaseq_era	3prime	poly_a	unknown	sc	single_cell_droplet	10x	France	2022-05-20	Adult	Adult	Heart	Cardiovascular System
11020	11020	ERR9750934	ERX9298873	ERS12023659	ERP137743	PRJEB52989	scRNAseq of post amputation regenerating zebrafish cardiac ventricle	E-MTAB-10643	Transcriptome Analysis	Adult zebrafish hearts have the ability to regenerate. The roles of non myocytes in this process have remained elusive. Here we have performed 2 scRNAseq experiments on interstitial cells. Experiment 1 E1 included interstitial cells obtained from uninjured regenerating 3 days 7 days and 14 days post apical amputation. Experiment 2 E2 included cells from uninjured sham operated abdomen opened and regenerating 3 dy post amputation with and without xxx inhibitor NSC40520 treatment. Cells were obtained by heart dissection followed by enzymatic dissociation and FACS sorting of single viable nucleated cells.	ENA FIRST PUBLIC:2022 05 20\|ENA LAST UPDATE:2022 05 20	Protocols: Zebrafish were euthanized in tricaine and hearts were extracted in PBS Hearts were pooled and pre digested for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this tissue was gently dissociated and passed through a cell strainer 40um spun down 5min 300g and resuspended in HBSS 2% fetal calf serum. The heart was exposed and approximately 20% of the ventricle removed Zebrafish were treated with MMP inhibitor NSC405020 for three days following surgery. Amplified cDNA was used for three prime RNA seq library generation RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.	Expt 3 3d post amputation + MMP inhibitor	SAMEA14418101	IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.	ENA first public:2022 05 20\|ENA last update:2022 05 20\|External Id:SAMEA14418101\|INSDC center alias:IGF CNRS INSERM Univ. Montpellier LabEx ICST F 34094 Montpellier France.\|INSDC center name:IGF CNRS INSERM Univ. Montpellier LabEx ICST F 34094 Montpellier France.\|INSDC first public:2022 05 20T16:17:49Z\|INSDC last update:2022 05 20T16:17:49Z\|INSDC status:public\|Submitter Id:E MTAB 10643:Expt 3 3d post amputation + MMP inhibitor\|age:6\|broker name:ArrayExpress\|cell type:interstitial cell\|common name:zebrafish\|developmental stage:adult\|genotype:wild type genotype\|injury:20 percent removal of the cardiac ventricle apex\|organism part:heart\|sample name:E MTAB 10643:Expt 3 3d post amputation + MMP inhibitor\|sex:male\|strain:AB\|treatment:matrix metalloproteinase inhibitor	Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle	E MTAB 10643:Expt 3 3d post amputation + MMP inhibitor p	Expt 3 3d post amputation + MMP inhibitor p	scRNAseq of post amputation regenerating zebrafish cardiac ventricle	Zebrafish were euthanized in tricaine and hearts were extracted in PBS "Hearts were pooled and ""pre digested"" for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this tissue was gently dissociated and passed through a cell strainer 40um spun down 5min 300g and resuspended in HBSS 2% fetal calf serum." The heart was exposed and approximately 20% of the ventricle removed Zebrafish were treated with MMP inhibitor NSC405020 for three days following surgery. Amplified cDNA was used for three prime RNA seq library generation RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.	Experimental Factor: injury:20 percent removal of the cardiac ventricle apex\|Experimental Factor: time:3\|Experimental Factor: treatment:matrix metalloproteinase inhibitor	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	SINGLE	ILLUMINA	Illumina NovaSeq 6000		ERP137743	Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle	ENA FIRST PUBLIC:2022 05 20\|ENA LAST UPDATE:2022 05 20	E2_3dpa_inhibitor_S4_L002_I1_001.fastq.gz E2_3dpa_inhibitor_S4_L002_I2_001.fastq.gz E2_3dpa_inhibitor_S4_L002_R1_001.fastq.gz E2_3dpa_inhibitor_S4_L002_R2_001.fastq.gz	fastq fastq fastq fastq	8621019270.0	63859402.0	E MTAB 10643:Expt 3 3d post amputation + MMP inhibitor	0:10 1:10 2:28 3:87	A:1438763050;C:1365497247;G:1350808021;T:1399773154;N:926502	10	10	28	87	1438763050	1365497247	1350808021	1399773154	926502	ERX9298873	ERS12023659	ERA14538536	IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.\|European Nucleotide Archive	IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.\|European Nucleotide Archive	1	0.92796		0.08671		0.87176		0.55088		87		B		usable mapping rate	illumina	novaseq_era	3prime	poly_a	unknown	sc	single_cell_droplet	10x	France	2022-05-20	Adult	Adult	Heart	Cardiovascular System
11021	11021	ERR9750933	ERX9298872	ERS12023658	ERP137743	PRJEB52989	scRNAseq of post amputation regenerating zebrafish cardiac ventricle	E-MTAB-10643	Transcriptome Analysis	Adult zebrafish hearts have the ability to regenerate. The roles of non myocytes in this process have remained elusive. Here we have performed 2 scRNAseq experiments on interstitial cells. Experiment 1 E1 included interstitial cells obtained from uninjured regenerating 3 days 7 days and 14 days post apical amputation. Experiment 2 E2 included cells from uninjured sham operated abdomen opened and regenerating 3 dy post amputation with and without xxx inhibitor NSC40520 treatment. Cells were obtained by heart dissection followed by enzymatic dissociation and FACS sorting of single viable nucleated cells.	ENA FIRST PUBLIC:2022 05 20\|ENA LAST UPDATE:2022 05 20	Protocols: Zebrafish were euthanized in tricaine and hearts were extracted in PBS Hearts were pooled and pre digested for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this tissue was gently dissociated and passed through a cell strainer 40um spun down 5min 300g and resuspended in HBSS 2% fetal calf serum. The heart was exposed and approximately 20% of the ventricle removed Amplified cDNA was used for three prime RNA seq library generation RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.	Expt 1 Uninjured	SAMEA14418100	IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.	ENA first public:2022 05 20\|ENA last update:2022 05 20\|External Id:SAMEA14418100\|INSDC center alias:IGF CNRS INSERM Univ. Montpellier LabEx ICST F 34094 Montpellier France.\|INSDC center name:IGF CNRS INSERM Univ. Montpellier LabEx ICST F 34094 Montpellier France.\|INSDC first public:2022 05 20T16:17:49Z\|INSDC last update:2022 05 20T16:17:49Z\|INSDC status:public\|Submitter Id:E MTAB 10643:Expt 1 Uninjured\|age:6\|broker name:ArrayExpress\|cell type:interstitial cell\|common name:zebrafish\|developmental stage:adult\|genotype:wild type genotype\|organism part:heart\|sample name:E MTAB 10643:Expt 1 Uninjured\|sex:male\|strain:AB	Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle	E MTAB 10643:Expt 1 Uninjured p	Expt 1 Uninjured p	scRNAseq of post amputation regenerating zebrafish cardiac ventricle	Zebrafish were euthanized in tricaine and hearts were extracted in PBS "Hearts were pooled and ""pre digested"" for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this tissue was gently dissociated and passed through a cell strainer 40um spun down 5min 300g and resuspended in HBSS 2% fetal calf serum." The heart was exposed and approximately 20% of the ventricle removed Amplified cDNA was used for three prime RNA seq library generation RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.	Experimental Factor: injury:n1\|Experimental Factor: treatment:n1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	SINGLE	ILLUMINA	Illumina NovaSeq 6000		ERP137743	Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle	ENA FIRST PUBLIC:2022 05 20\|ENA LAST UPDATE:2022 05 20	E1_Uninjured_S1_L002_I1_001.fastq.gz E1_Uninjured_S1_L002_R1_001.fastq.gz E1_Uninjured_S1_L002_R2_001.fastq.gz	fastq fastq fastq	8575585211.0	67524293.0	E MTAB 10643:Expt 1 Uninjured	0:8 1:28 2:91	A:1801503847;C:1312196506;G:1367890726;T:1663053783;N:65801	8	28	91		1801503847	1312196506	1367890726	1663053783	65801	ERX9298872	ERS12023658	ERA14538536	IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.\|European Nucleotide Archive	IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.\|European Nucleotide Archive	1	0.9169		0.11202		0.81576		0.54253		91		B		usable mapping rate	illumina	novaseq_era	3prime	poly_a	unknown	sc	single_cell_droplet	10x	France	2022-05-20	Adult	Adult	Heart	Cardiovascular System
11022	11022	ERR9750932	ERX9298871	ERS12023657	ERP137743	PRJEB52989	scRNAseq of post amputation regenerating zebrafish cardiac ventricle	E-MTAB-10643	Transcriptome Analysis	Adult zebrafish hearts have the ability to regenerate. The roles of non myocytes in this process have remained elusive. Here we have performed 2 scRNAseq experiments on interstitial cells. Experiment 1 E1 included interstitial cells obtained from uninjured regenerating 3 days 7 days and 14 days post apical amputation. Experiment 2 E2 included cells from uninjured sham operated abdomen opened and regenerating 3 dy post amputation with and without xxx inhibitor NSC40520 treatment. Cells were obtained by heart dissection followed by enzymatic dissociation and FACS sorting of single viable nucleated cells.	ENA FIRST PUBLIC:2022 05 20\|ENA LAST UPDATE:2022 05 20	Protocols: Zebrafish were euthanized in tricaine and hearts were extracted in PBS Hearts were pooled and pre digested for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this tissue was gently dissociated and passed through a cell strainer 40um spun down 5min 300g and resuspended in HBSS 2% fetal calf serum. The heart was exposed and approximately 20% of the ventricle removed Amplified cDNA was used for three prime RNA seq library generation RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.	Expt 1 7d post amputation	SAMEA14418099	IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.	ENA first public:2022 05 20\|ENA last update:2022 05 20\|External Id:SAMEA14418099\|INSDC center alias:IGF CNRS INSERM Univ. Montpellier LabEx ICST F 34094 Montpellier France.\|INSDC center name:IGF CNRS INSERM Univ. Montpellier LabEx ICST F 34094 Montpellier France.\|INSDC first public:2022 05 20T16:17:49Z\|INSDC last update:2022 05 20T16:17:49Z\|INSDC status:public\|Submitter Id:E MTAB 10643:Expt 1 7d post amputation\|age:6\|broker name:ArrayExpress\|cell type:interstitial cell\|common name:zebrafish\|developmental stage:adult\|genotype:wild type genotype\|injury:20 percent removal of the cardiac ventricle apex\|organism part:heart\|sample name:E MTAB 10643:Expt 1 7d post amputation\|sex:male\|strain:AB	Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle	E MTAB 10643:Expt 1 7d post amputation p	Expt 1 7d post amputation p	scRNAseq of post amputation regenerating zebrafish cardiac ventricle	Zebrafish were euthanized in tricaine and hearts were extracted in PBS "Hearts were pooled and ""pre digested"" for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this tissue was gently dissociated and passed through a cell strainer 40um spun down 5min 300g and resuspended in HBSS 2% fetal calf serum." The heart was exposed and approximately 20% of the ventricle removed Amplified cDNA was used for three prime RNA seq library generation RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.	Experimental Factor: injury:20 percent removal of the cardiac ventricle apex\|Experimental Factor: time:7\|Experimental Factor: treatment:n1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	SINGLE	ILLUMINA	Illumina NovaSeq 6000		ERP137743	Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle	ENA FIRST PUBLIC:2022 05 20\|ENA LAST UPDATE:2022 05 20	E1_7d_S3_L002_I1_001.fastq.gz E1_7d_S3_L002_R1_001.fastq.gz E1_7d_S3_L002_R2_001.fastq.gz	fastq fastq fastq	17341796660.0	136549580.0	E MTAB 10643:Expt 1 7d post amputation	0:8 1:28 2:91	A:3506600812;C:2774617588;G:2814960106;T:3329701112;N:132162	8	28	91		3506600812	2774617588	2814960106	3329701112	132162	ERX9298871	ERS12023657	ERA14538536	IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.\|European Nucleotide Archive	IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.\|European Nucleotide Archive	1	0.90616		0.09608		0.82446		0.46632		91		B		usable mapping rate	illumina	novaseq_era	3prime	poly_a	unknown	sc	single_cell_droplet	10x	France	2022-05-20	Adult	Adult	Heart	Cardiovascular System
11023	11023	ERR9750931	ERX9298870	ERS12023656	ERP137743	PRJEB52989	scRNAseq of post amputation regenerating zebrafish cardiac ventricle	E-MTAB-10643	Transcriptome Analysis	Adult zebrafish hearts have the ability to regenerate. The roles of non myocytes in this process have remained elusive. Here we have performed 2 scRNAseq experiments on interstitial cells. Experiment 1 E1 included interstitial cells obtained from uninjured regenerating 3 days 7 days and 14 days post apical amputation. Experiment 2 E2 included cells from uninjured sham operated abdomen opened and regenerating 3 dy post amputation with and without xxx inhibitor NSC40520 treatment. Cells were obtained by heart dissection followed by enzymatic dissociation and FACS sorting of single viable nucleated cells.	ENA FIRST PUBLIC:2022 05 20\|ENA LAST UPDATE:2022 05 20	Protocols: Zebrafish were euthanized in tricaine and hearts were extracted in PBS Hearts were pooled and pre digested for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this tissue was gently dissociated and passed through a cell strainer 40um spun down 5min 300g and resuspended in HBSS 2% fetal calf serum. The heart was exposed and approximately 20% of the ventricle removed Amplified cDNA was used for three prime RNA seq library generation RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.	Expt 1 3d post amputation	SAMEA14418098	IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.	ENA first public:2022 05 20\|ENA last update:2022 05 20\|External Id:SAMEA14418098\|INSDC center alias:IGF CNRS INSERM Univ. Montpellier LabEx ICST F 34094 Montpellier France.\|INSDC center name:IGF CNRS INSERM Univ. Montpellier LabEx ICST F 34094 Montpellier France.\|INSDC first public:2022 05 20T16:17:49Z\|INSDC last update:2022 05 20T16:17:49Z\|INSDC status:public\|Submitter Id:E MTAB 10643:Expt 1 3d post amputation\|age:6\|broker name:ArrayExpress\|cell type:interstitial cell\|common name:zebrafish\|developmental stage:adult\|genotype:wild type genotype\|injury:20 percent removal of the cardiac ventricle apex\|organism part:heart\|sample name:E MTAB 10643:Expt 1 3d post amputation\|sex:male\|strain:AB	Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle	E MTAB 10643:Expt 1 3d post amputation p	Expt 1 3d post amputation p	scRNAseq of post amputation regenerating zebrafish cardiac ventricle	Zebrafish were euthanized in tricaine and hearts were extracted in PBS "Hearts were pooled and ""pre digested"" for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this tissue was gently dissociated and passed through a cell strainer 40um spun down 5min 300g and resuspended in HBSS 2% fetal calf serum." The heart was exposed and approximately 20% of the ventricle removed Amplified cDNA was used for three prime RNA seq library generation RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.	Experimental Factor: injury:20 percent removal of the cardiac ventricle apex\|Experimental Factor: time:3\|Experimental Factor: treatment:n1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	SINGLE	ILLUMINA	Illumina NovaSeq 6000		ERP137743	Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle	ENA FIRST PUBLIC:2022 05 20\|ENA LAST UPDATE:2022 05 20	E1_3d_S2_L002_I1_001.fastq.gz E1_3d_S2_L002_R1_001.fastq.gz E1_3d_S2_L002_R2_001.fastq.gz	fastq fastq fastq	8183008018.0	64433134.0	E MTAB 10643:Expt 1 3d post amputation	0:8 1:28 2:91	A:1630460899;C:1330248096;G:1326144211;T:1576499358;N:62630	8	28	91		1630460899	1330248096	1326144211	1576499358	62630	ERX9298870	ERS12023656	ERA14538536	IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.\|European Nucleotide Archive	IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.\|European Nucleotide Archive	1	0.88759		0.08679		0.82948		0.47863		91		B		usable mapping rate	illumina	novaseq_era	3prime	poly_a	unknown	sc	single_cell_droplet	10x	France	2022-05-20	Adult	Adult	Heart	Cardiovascular System
11024	11024	ERR9750930	ERX9298869	ERS12023655	ERP137743	PRJEB52989	scRNAseq of post amputation regenerating zebrafish cardiac ventricle	E-MTAB-10643	Transcriptome Analysis	Adult zebrafish hearts have the ability to regenerate. The roles of non myocytes in this process have remained elusive. Here we have performed 2 scRNAseq experiments on interstitial cells. Experiment 1 E1 included interstitial cells obtained from uninjured regenerating 3 days 7 days and 14 days post apical amputation. Experiment 2 E2 included cells from uninjured sham operated abdomen opened and regenerating 3 dy post amputation with and without xxx inhibitor NSC40520 treatment. Cells were obtained by heart dissection followed by enzymatic dissociation and FACS sorting of single viable nucleated cells.	ENA FIRST PUBLIC:2022 05 20\|ENA LAST UPDATE:2022 05 20	Protocols: Zebrafish were euthanized in tricaine and hearts were extracted in PBS Hearts were pooled and pre digested for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this tissue was gently dissociated and passed through a cell strainer 40um spun down 5min 300g and resuspended in HBSS 2% fetal calf serum. The heart was exposed and approximately 20% of the ventricle removed Amplified cDNA was used for three prime RNA seq library generation RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.	Expt 1 14d post amputation	SAMEA14418097	IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.	ENA first public:2022 05 20\|ENA last update:2022 05 20\|External Id:SAMEA14418097\|INSDC center alias:IGF CNRS INSERM Univ. Montpellier LabEx ICST F 34094 Montpellier France.\|INSDC center name:IGF CNRS INSERM Univ. Montpellier LabEx ICST F 34094 Montpellier France.\|INSDC first public:2022 05 20T16:17:49Z\|INSDC last update:2022 05 20T16:17:49Z\|INSDC status:public\|Submitter Id:E MTAB 10643:Expt 1 14d post amputation\|age:6\|broker name:ArrayExpress\|cell type:interstitial cell\|common name:zebrafish\|developmental stage:adult\|genotype:wild type genotype\|injury:20 percent removal of the cardiac ventricle apex\|organism part:heart\|sample name:E MTAB 10643:Expt 1 14d post amputation\|sex:male\|strain:AB	Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle	E MTAB 10643:Expt 1 14d post amputation p	Expt 1 14d post amputation p	scRNAseq of post amputation regenerating zebrafish cardiac ventricle	Zebrafish were euthanized in tricaine and hearts were extracted in PBS "Hearts were pooled and ""pre digested"" for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this tissue was gently dissociated and passed through a cell strainer 40um spun down 5min 300g and resuspended in HBSS 2% fetal calf serum." The heart was exposed and approximately 20% of the ventricle removed Amplified cDNA was used for three prime RNA seq library generation RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.	Experimental Factor: injury:20 percent removal of the cardiac ventricle apex\|Experimental Factor: time:14\|Experimental Factor: treatment:n1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	SINGLE	ILLUMINA	Illumina NovaSeq 6000		ERP137743	Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle	ENA FIRST PUBLIC:2022 05 20\|ENA LAST UPDATE:2022 05 20	E1_14d_S4_L002_I1_001.fastq.gz E1_14d_S4_L002_R1_001.fastq.gz E1_14d_S4_L002_R2_001.fastq.gz	fastq fastq fastq	12911908390.0	101668570.0	E MTAB 10643:Expt 1 14d post amputation	0:8 1:28 2:91	A:2700371496;C:1971281481;G:2062280628;T:2517806408;N:99857	8	28	91		2700371496	1971281481	2062280628	2517806408	99857	ERX9298869	ERS12023655	ERA14538536	IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.\|European Nucleotide Archive	IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.\|European Nucleotide Archive	1	0.90771		0.11048		0.81523		0.53024		91		B		usable mapping rate	illumina	novaseq_era	3prime	poly_a	unknown	sc	single_cell_droplet	10x	France	2022-05-20	Adult	Adult	Heart	Cardiovascular System
11711	11711	ERR11282347	ERX10689990	ERS15395535	ERP146895	PRJEB61813	RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month	E-MTAB-12901	Other	The ATP binding cassette subfamily B member 1 ABCB1 encoding a multidrug transporter P glycoprotein plays a critical role in the efflux of xenobiotics in humans and is implicated in cancer resistance to chemotherapy—however little information regarding Pgp at the zebrafish. In addition to study the function of Pgp in the zebrafish brain in the aging process we performed RNA seq using brain tissue of WT and abcb4 knockout zebrafish at different ages such as 2 month and 30 month.	ENA FIRST PUBLIC:2023 07 14\|ENA LAST UPDATE:2023 07 14	Protocols: brain tissue were dissected from zebrafish and snap frozen until RNA isolation Trizol + zymo RNA clean column kit TruSeq RNA sample prep kit Illumina to prepare cDNA libraries post PolyA selection	Sample 8	SAMEA113400389	VANDERBILT UNIVERSITY	ENA FIRST PUBLIC:2023 07 14T00:23:41Z\|ENA LAST UPDATE:2023 07 14T00:23:41Z\|External Id:SAMEA113400389\|INSDC center alias:VANDERBILT UNIVERSITY\|INSDC center name:VANDERBILT UNIVERSITY\|INSDC first public:2023 07 14T00:23:41Z\|INSDC last update:2023 07 14T00:23:41Z\|INSDC status:public\|Submitter Id:E MTAB 12901:Sample 8\|age:2\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|disease:normal\|genotype:wild type genotype\|organism part:brain\|sample name:E MTAB 12901:Sample 8\|scientific name:Danio rerio\|sex:female\|strain:AB	Illumina NovaSeq 6000 paired end sequencing; RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month	E MTAB 12901:Sample 8 p	Sample 8 p	RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month	brain tissue were dissected from zebrafish and snap frozen until RNA isolation Trizol + zymo RNA clean column kit TruSeq RNA sample prep kit Illumina to prepare cDNA libraries post PolyA selection	Experimental Factor: genotype:wild type genotype	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP146895	Illumina NovaSeq 6000 paired end sequencing; RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month	ENA FIRST PUBLIC:2023 07 14\|ENA LAST UPDATE:2023 07 14	8680-JP-0008_S1_L005_R2_001.fastq.gz 8680-JP-0008_S1_L005_R1_001.fastq.gz	fastq fastq	21919844332.0	72582266.0	E MTAB 12901:8680 JP 0008 S1 L005 R	0:151 1:151	A:5996325335;C:4770833694;G:5244802952;T:5876120950;N:31761401	151	151			5996325335	4770833694	5244802952	5876120950	31761401	ERX10689990	ERS15395535	ERA23235100	VANDERBILT UNIVERSITY\|European Nucleotide Archive	VANDERBILT UNIVERSITY\|European Nucleotide Archive	2	0.92572	0.92425	0.13427	0.13101	0.70086	0.70266	0.50868	0.50381	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2023-07-14	Adult	Adult	Brain	Nervous System
11712	11712	ERR11282346	ERX10689989	ERS15395534	ERP146895	PRJEB61813	RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month	E-MTAB-12901	Other	The ATP binding cassette subfamily B member 1 ABCB1 encoding a multidrug transporter P glycoprotein plays a critical role in the efflux of xenobiotics in humans and is implicated in cancer resistance to chemotherapy—however little information regarding Pgp at the zebrafish. In addition to study the function of Pgp in the zebrafish brain in the aging process we performed RNA seq using brain tissue of WT and abcb4 knockout zebrafish at different ages such as 2 month and 30 month.	ENA FIRST PUBLIC:2023 07 14\|ENA LAST UPDATE:2023 07 14	Protocols: brain tissue were dissected from zebrafish and snap frozen until RNA isolation Trizol + zymo RNA clean column kit TruSeq RNA sample prep kit Illumina to prepare cDNA libraries post PolyA selection	Sample 7	SAMEA113400388	VANDERBILT UNIVERSITY	ENA FIRST PUBLIC:2023 07 14T00:23:41Z\|ENA LAST UPDATE:2023 07 14T00:23:41Z\|External Id:SAMEA113400388\|INSDC center alias:VANDERBILT UNIVERSITY\|INSDC center name:VANDERBILT UNIVERSITY\|INSDC first public:2023 07 14T00:23:41Z\|INSDC last update:2023 07 14T00:23:41Z\|INSDC status:public\|Submitter Id:E MTAB 12901:Sample 7\|age:2\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|disease:normal\|genotype:wild type genotype\|organism part:brain\|sample name:E MTAB 12901:Sample 7\|scientific name:Danio rerio\|sex:female\|strain:AB	Illumina NovaSeq 6000 paired end sequencing; RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month	E MTAB 12901:Sample 7 p	Sample 7 p	RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month	brain tissue were dissected from zebrafish and snap frozen until RNA isolation Trizol + zymo RNA clean column kit TruSeq RNA sample prep kit Illumina to prepare cDNA libraries post PolyA selection	Experimental Factor: genotype:wild type genotype	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP146895	Illumina NovaSeq 6000 paired end sequencing; RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month	ENA FIRST PUBLIC:2023 07 14\|ENA LAST UPDATE:2023 07 14	8680-JP-0007_S1_L005_R2_001.fastq.gz 8680-JP-0007_S1_L005_R1_001.fastq.gz	fastq fastq	20351465316.0	67388958.0	E MTAB 12901:8680 JP 0007 S1 L005 R	0:151 1:151	A:5563989836;C:4461170993;G:4892290448;T:5404916249;N:29097790	151	151			5563989836	4461170993	4892290448	5404916249	29097790	ERX10689989	ERS15395534	ERA23235100	VANDERBILT UNIVERSITY\|European Nucleotide Archive	VANDERBILT UNIVERSITY\|European Nucleotide Archive	2	0.9267	0.9236	0.12782	0.12528	0.70307	0.70473	0.50799	0.50969	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2023-07-14	Adult	Adult	Brain	Nervous System
11713	11713	ERR11282345	ERX10689988	ERS15395533	ERP146895	PRJEB61813	RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month	E-MTAB-12901	Other	The ATP binding cassette subfamily B member 1 ABCB1 encoding a multidrug transporter P glycoprotein plays a critical role in the efflux of xenobiotics in humans and is implicated in cancer resistance to chemotherapy—however little information regarding Pgp at the zebrafish. In addition to study the function of Pgp in the zebrafish brain in the aging process we performed RNA seq using brain tissue of WT and abcb4 knockout zebrafish at different ages such as 2 month and 30 month.	ENA FIRST PUBLIC:2023 07 14\|ENA LAST UPDATE:2023 07 14	Protocols: brain tissue were dissected from zebrafish and snap frozen until RNA isolation Trizol + zymo RNA clean column kit TruSeq RNA sample prep kit Illumina to prepare cDNA libraries post PolyA selection	Sample 6	SAMEA113400387	VANDERBILT UNIVERSITY	ENA FIRST PUBLIC:2023 07 14T00:23:41Z\|ENA LAST UPDATE:2023 07 14T00:23:41Z\|External Id:SAMEA113400387\|INSDC center alias:VANDERBILT UNIVERSITY\|INSDC center name:VANDERBILT UNIVERSITY\|INSDC first public:2023 07 14T00:23:41Z\|INSDC last update:2023 07 14T00:23:41Z\|INSDC status:public\|Submitter Id:E MTAB 12901:Sample 6\|age:2\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|disease:normal\|genotype:wild type genotype\|organism part:brain\|sample name:E MTAB 12901:Sample 6\|scientific name:Danio rerio\|sex:female\|strain:AB	Illumina NovaSeq 6000 paired end sequencing; RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month	E MTAB 12901:Sample 6 p	Sample 6 p	RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month	brain tissue were dissected from zebrafish and snap frozen until RNA isolation Trizol + zymo RNA clean column kit TruSeq RNA sample prep kit Illumina to prepare cDNA libraries post PolyA selection	Experimental Factor: genotype:wild type genotype	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP146895	Illumina NovaSeq 6000 paired end sequencing; RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month	ENA FIRST PUBLIC:2023 07 14\|ENA LAST UPDATE:2023 07 14	8680-JP-0006_S1_L005_R2_001.fastq.gz 8680-JP-0006_S1_L005_R1_001.fastq.gz	fastq fastq	19220102648.0	63642724.0	E MTAB 12901:8680 JP 0006 S1 L005 R	0:151 1:151	A:5250476003;C:4214339559;G:4606611173;T:5120701154;N:27974759	151	151			5250476003	4214339559	4606611173	5120701154	27974759	ERX10689988	ERS15395533	ERA23235100	VANDERBILT UNIVERSITY\|European Nucleotide Archive	VANDERBILT UNIVERSITY\|European Nucleotide Archive	2	0.92441	0.92391	0.13718	0.13346	0.70281	0.7024	0.48155	0.49173	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2023-07-14	Adult	Adult	Brain	Nervous System
11714	11714	ERR11282344	ERX10689987	ERS15395532	ERP146895	PRJEB61813	RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month	E-MTAB-12901	Other	The ATP binding cassette subfamily B member 1 ABCB1 encoding a multidrug transporter P glycoprotein plays a critical role in the efflux of xenobiotics in humans and is implicated in cancer resistance to chemotherapy—however little information regarding Pgp at the zebrafish. In addition to study the function of Pgp in the zebrafish brain in the aging process we performed RNA seq using brain tissue of WT and abcb4 knockout zebrafish at different ages such as 2 month and 30 month.	ENA FIRST PUBLIC:2023 07 14\|ENA LAST UPDATE:2023 07 14	Protocols: brain tissue were dissected from zebrafish and snap frozen until RNA isolation Trizol + zymo RNA clean column kit TruSeq RNA sample prep kit Illumina to prepare cDNA libraries post PolyA selection	Sample 3	SAMEA113400386	VANDERBILT UNIVERSITY	ENA FIRST PUBLIC:2023 07 14T00:23:41Z\|ENA LAST UPDATE:2023 07 14T00:23:41Z\|External Id:SAMEA113400386\|INSDC center alias:VANDERBILT UNIVERSITY\|INSDC center name:VANDERBILT UNIVERSITY\|INSDC first public:2023 07 14T00:23:41Z\|INSDC last update:2023 07 14T00:23:41Z\|INSDC status:public\|Submitter Id:E MTAB 12901:Sample 3\|age:30\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|disease:normal\|genotype:wild type genotype\|organism part:brain\|sample name:E MTAB 12901:Sample 3\|scientific name:Danio rerio\|sex:female\|strain:AB	Illumina NovaSeq 6000 paired end sequencing; RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month	E MTAB 12901:Sample 3 p	Sample 3 p	RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month	brain tissue were dissected from zebrafish and snap frozen until RNA isolation Trizol + zymo RNA clean column kit TruSeq RNA sample prep kit Illumina to prepare cDNA libraries post PolyA selection	Experimental Factor: genotype:wild type genotype	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP146895	Illumina NovaSeq 6000 paired end sequencing; RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month	ENA FIRST PUBLIC:2023 07 14\|ENA LAST UPDATE:2023 07 14	8680-JP-0003_S1_L005_R1_001.fastq.gz 8680-JP-0003_S1_L005_R2_001.fastq.gz	fastq fastq	18624364462.0	61670081.0	E MTAB 12901:8680 JP 0003 S1 L005 R	0:151 1:151	A:5114421711;C:4075705896;G:4436341056;T:4970953410;N:26942389	151	151			5114421711	4075705896	4436341056	4970953410	26942389	ERX10689987	ERS15395532	ERA23235100	VANDERBILT UNIVERSITY\|European Nucleotide Archive	VANDERBILT UNIVERSITY\|European Nucleotide Archive	2	0.92553	0.92378	0.13069	0.12709	0.69988	0.70258	0.4969	0.51157	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2023-07-14	Adult	Adult	Brain	Nervous System
11715	11715	ERR11282343	ERX10689986	ERS15395531	ERP146895	PRJEB61813	RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month	E-MTAB-12901	Other	The ATP binding cassette subfamily B member 1 ABCB1 encoding a multidrug transporter P glycoprotein plays a critical role in the efflux of xenobiotics in humans and is implicated in cancer resistance to chemotherapy—however little information regarding Pgp at the zebrafish. In addition to study the function of Pgp in the zebrafish brain in the aging process we performed RNA seq using brain tissue of WT and abcb4 knockout zebrafish at different ages such as 2 month and 30 month.	ENA FIRST PUBLIC:2023 07 14\|ENA LAST UPDATE:2023 07 14	Protocols: brain tissue were dissected from zebrafish and snap frozen until RNA isolation Trizol + zymo RNA clean column kit TruSeq RNA sample prep kit Illumina to prepare cDNA libraries post PolyA selection	Sample 2	SAMEA113400385	VANDERBILT UNIVERSITY	ENA FIRST PUBLIC:2023 07 14T00:23:41Z\|ENA LAST UPDATE:2023 07 14T00:23:41Z\|External Id:SAMEA113400385\|INSDC center alias:VANDERBILT UNIVERSITY\|INSDC center name:VANDERBILT UNIVERSITY\|INSDC first public:2023 07 14T00:23:41Z\|INSDC last update:2023 07 14T00:23:41Z\|INSDC status:public\|Submitter Id:E MTAB 12901:Sample 2\|age:30\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|disease:normal\|genotype:wild type genotype\|organism part:brain\|sample name:E MTAB 12901:Sample 2\|scientific name:Danio rerio\|sex:female\|strain:AB	Illumina NovaSeq 6000 paired end sequencing; RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month	E MTAB 12901:Sample 2 p	Sample 2 p	RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month	brain tissue were dissected from zebrafish and snap frozen until RNA isolation Trizol + zymo RNA clean column kit TruSeq RNA sample prep kit Illumina to prepare cDNA libraries post PolyA selection	Experimental Factor: genotype:wild type genotype	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP146895	Illumina NovaSeq 6000 paired end sequencing; RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month	ENA FIRST PUBLIC:2023 07 14\|ENA LAST UPDATE:2023 07 14	8680-JP-0002_S1_L005_R1_001.fastq.gz 8680-JP-0002_S1_L005_R2_001.fastq.gz	fastq fastq	15153807038.0	50178169.0	E MTAB 12901:8680 JP 0002 S1 L005 R	0:151 1:151	A:4156183785;C:3309476575;G:3635942314;T:4030261947;N:21942417	151	151			4156183785	3309476575	3635942314	4030261947	21942417	ERX10689986	ERS15395531	ERA23235100	VANDERBILT UNIVERSITY\|European Nucleotide Archive	VANDERBILT UNIVERSITY\|European Nucleotide Archive	2	0.92069	0.91964	0.13733	0.13466	0.70102	0.70185	0.48507	0.48992	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2023-07-14	Adult	Adult	Brain	Nervous System
11716	11716	ERR11282342	ERX10689985	ERS15395530	ERP146895	PRJEB61813	RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month	E-MTAB-12901	Other	The ATP binding cassette subfamily B member 1 ABCB1 encoding a multidrug transporter P glycoprotein plays a critical role in the efflux of xenobiotics in humans and is implicated in cancer resistance to chemotherapy—however little information regarding Pgp at the zebrafish. In addition to study the function of Pgp in the zebrafish brain in the aging process we performed RNA seq using brain tissue of WT and abcb4 knockout zebrafish at different ages such as 2 month and 30 month.	ENA FIRST PUBLIC:2023 07 14\|ENA LAST UPDATE:2023 07 14	Protocols: brain tissue were dissected from zebrafish and snap frozen until RNA isolation Trizol + zymo RNA clean column kit TruSeq RNA sample prep kit Illumina to prepare cDNA libraries post PolyA selection	Sample 1	SAMEA113400384	VANDERBILT UNIVERSITY	ENA FIRST PUBLIC:2023 07 14T00:23:41Z\|ENA LAST UPDATE:2023 07 14T00:23:41Z\|External Id:SAMEA113400384\|INSDC center alias:VANDERBILT UNIVERSITY\|INSDC center name:VANDERBILT UNIVERSITY\|INSDC first public:2023 07 14T00:23:41Z\|INSDC last update:2023 07 14T00:23:41Z\|INSDC status:public\|Submitter Id:E MTAB 12901:Sample 1\|age:30\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|disease:normal\|genotype:wild type genotype\|organism part:brain\|sample name:E MTAB 12901:Sample 1\|scientific name:Danio rerio\|sex:female\|strain:AB	Illumina NovaSeq 6000 paired end sequencing; RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month	E MTAB 12901:Sample 1 p	Sample 1 p	RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month	brain tissue were dissected from zebrafish and snap frozen until RNA isolation Trizol + zymo RNA clean column kit TruSeq RNA sample prep kit Illumina to prepare cDNA libraries post PolyA selection	Experimental Factor: genotype:wild type genotype	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP146895	Illumina NovaSeq 6000 paired end sequencing; RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month	ENA FIRST PUBLIC:2023 07 14\|ENA LAST UPDATE:2023 07 14	8680-JP-0001_S1_L005_R2_001.fastq.gz 8680-JP-0001_S1_L005_R1_001.fastq.gz	fastq fastq	17758550696.0	58803148.0	E MTAB 12901:8680 JP 0001 S1 L005 R	0:151 1:151	A:4866917250;C:3906782394;G:4241519777;T:4717566830;N:25764445	151	151			4866917250	3906782394	4241519777	4717566830	25764445	ERX10689985	ERS15395530	ERA23235100	VANDERBILT UNIVERSITY\|European Nucleotide Archive	VANDERBILT UNIVERSITY\|European Nucleotide Archive	2	0.92263	0.92154	0.13341	0.12969	0.69443	0.69658	0.48648	0.49678	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2023-07-14	Adult	Adult	Brain	Nervous System
11717	11717	ERR11282341	ERX10689984	ERS15395529	ERP146895	PRJEB61813	RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month	E-MTAB-12901	Other	The ATP binding cassette subfamily B member 1 ABCB1 encoding a multidrug transporter P glycoprotein plays a critical role in the efflux of xenobiotics in humans and is implicated in cancer resistance to chemotherapy—however little information regarding Pgp at the zebrafish. In addition to study the function of Pgp in the zebrafish brain in the aging process we performed RNA seq using brain tissue of WT and abcb4 knockout zebrafish at different ages such as 2 month and 30 month.	ENA FIRST PUBLIC:2023 07 14\|ENA LAST UPDATE:2023 07 14	Protocols: brain tissue were dissected from zebrafish and snap frozen until RNA isolation Trizol + zymo RNA clean column kit TruSeq RNA sample prep kit Illumina to prepare cDNA libraries post PolyA selection	Sample 9	SAMEA113400383	VANDERBILT UNIVERSITY	ENA FIRST PUBLIC:2023 07 14T00:23:41Z\|ENA LAST UPDATE:2023 07 14T00:23:41Z\|External Id:SAMEA113400383\|INSDC center alias:VANDERBILT UNIVERSITY\|INSDC center name:VANDERBILT UNIVERSITY\|INSDC first public:2023 07 14T00:23:41Z\|INSDC last update:2023 07 14T00:23:41Z\|INSDC status:public\|Submitter Id:E MTAB 12901:Sample 9\|age:2\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|disease:normal\|genotype:abcb4 / \|organism part:brain\|sample name:E MTAB 12901:Sample 9\|scientific name:Danio rerio\|sex:female\|strain:AB	Illumina NovaSeq 6000 paired end sequencing; RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month	E MTAB 12901:Sample 9 p	Sample 9 p	RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month	brain tissue were dissected from zebrafish and snap frozen until RNA isolation Trizol + zymo RNA clean column kit TruSeq RNA sample prep kit Illumina to prepare cDNA libraries post PolyA selection	Experimental Factor: genotype:abcb4 /	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP146895	Illumina NovaSeq 6000 paired end sequencing; RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month	ENA FIRST PUBLIC:2023 07 14\|ENA LAST UPDATE:2023 07 14	8680-JP-0009_S1_L005_R2_001.fastq.gz 8680-JP-0009_S1_L005_R1_001.fastq.gz	fastq fastq	21619735456.0	71588528.0	E MTAB 12901:8680 JP 0009 S1 L005 R	0:151 1:151	A:5904040180;C:4720941204;G:5229712921;T:5733559571;N:31481580	151	151			5904040180	4720941204	5229712921	5733559571	31481580	ERX10689984	ERS15395529	ERA23235100	VANDERBILT UNIVERSITY\|European Nucleotide Archive	VANDERBILT UNIVERSITY\|European Nucleotide Archive	2	0.92235	0.92126	0.13956	0.13682	0.70378	0.70526	0.4929	0.49286	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2023-07-14	Adult	Adult	Brain	Nervous System
11718	11718	ERR11282340	ERX10689983	ERS15395528	ERP146895	PRJEB61813	RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month	E-MTAB-12901	Other	The ATP binding cassette subfamily B member 1 ABCB1 encoding a multidrug transporter P glycoprotein plays a critical role in the efflux of xenobiotics in humans and is implicated in cancer resistance to chemotherapy—however little information regarding Pgp at the zebrafish. In addition to study the function of Pgp in the zebrafish brain in the aging process we performed RNA seq using brain tissue of WT and abcb4 knockout zebrafish at different ages such as 2 month and 30 month.	ENA FIRST PUBLIC:2023 07 14\|ENA LAST UPDATE:2023 07 14	Protocols: brain tissue were dissected from zebrafish and snap frozen until RNA isolation Trizol + zymo RNA clean column kit TruSeq RNA sample prep kit Illumina to prepare cDNA libraries post PolyA selection	Sample 11	SAMEA113400382	VANDERBILT UNIVERSITY	ENA FIRST PUBLIC:2023 07 14T00:23:41Z\|ENA LAST UPDATE:2023 07 14T00:23:41Z\|External Id:SAMEA113400382\|INSDC center alias:VANDERBILT UNIVERSITY\|INSDC center name:VANDERBILT UNIVERSITY\|INSDC first public:2023 07 14T00:23:41Z\|INSDC last update:2023 07 14T00:23:41Z\|INSDC status:public\|Submitter Id:E MTAB 12901:Sample 11\|age:2\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|disease:normal\|genotype:abcb4 / \|organism part:brain\|sample name:E MTAB 12901:Sample 11\|scientific name:Danio rerio\|sex:female\|strain:AB	Illumina NovaSeq 6000 paired end sequencing; RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month	E MTAB 12901:Sample 11 p	Sample 11 p	RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month	brain tissue were dissected from zebrafish and snap frozen until RNA isolation Trizol + zymo RNA clean column kit TruSeq RNA sample prep kit Illumina to prepare cDNA libraries post PolyA selection	Experimental Factor: genotype:abcb4 /	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP146895	Illumina NovaSeq 6000 paired end sequencing; RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month	ENA FIRST PUBLIC:2023 07 14\|ENA LAST UPDATE:2023 07 14	8680-JP-0011_S1_L005_R1_001.fastq.gz 8680-JP-0011_S1_L005_R2_001.fastq.gz	fastq fastq	20372991574.0	67460237.0	E MTAB 12901:8680 JP 0011 S1 L005 R	0:151 1:151	A:5569250549;C:4448986210;G:4925237941;T:5399892024;N:29624850	151	151			5569250549	4448986210	4925237941	5399892024	29624850	ERX10689983	ERS15395528	ERA23235100	VANDERBILT UNIVERSITY\|European Nucleotide Archive	VANDERBILT UNIVERSITY\|European Nucleotide Archive	2	0.92578	0.92449	0.12979	0.12632	0.69666	0.69775	0.51379	0.51557	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2023-07-14	Adult	Adult	Brain	Nervous System
11719	11719	ERR11282339	ERX10689982	ERS15395527	ERP146895	PRJEB61813	RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month	E-MTAB-12901	Other	The ATP binding cassette subfamily B member 1 ABCB1 encoding a multidrug transporter P glycoprotein plays a critical role in the efflux of xenobiotics in humans and is implicated in cancer resistance to chemotherapy—however little information regarding Pgp at the zebrafish. In addition to study the function of Pgp in the zebrafish brain in the aging process we performed RNA seq using brain tissue of WT and abcb4 knockout zebrafish at different ages such as 2 month and 30 month.	ENA FIRST PUBLIC:2023 07 14\|ENA LAST UPDATE:2023 07 14	Protocols: brain tissue were dissected from zebrafish and snap frozen until RNA isolation Trizol + zymo RNA clean column kit TruSeq RNA sample prep kit Illumina to prepare cDNA libraries post PolyA selection	Sample 10	SAMEA113400381	VANDERBILT UNIVERSITY	ENA FIRST PUBLIC:2023 07 14T00:23:41Z\|ENA LAST UPDATE:2023 07 14T00:23:41Z\|External Id:SAMEA113400381\|INSDC center alias:VANDERBILT UNIVERSITY\|INSDC center name:VANDERBILT UNIVERSITY\|INSDC first public:2023 07 14T00:23:41Z\|INSDC last update:2023 07 14T00:23:41Z\|INSDC status:public\|Submitter Id:E MTAB 12901:Sample 10\|age:2\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|disease:normal\|genotype:abcb4 / \|organism part:brain\|sample name:E MTAB 12901:Sample 10\|scientific name:Danio rerio\|sex:female\|strain:AB	Illumina NovaSeq 6000 paired end sequencing; RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month	E MTAB 12901:Sample 10 p	Sample 10 p	RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month	brain tissue were dissected from zebrafish and snap frozen until RNA isolation Trizol + zymo RNA clean column kit TruSeq RNA sample prep kit Illumina to prepare cDNA libraries post PolyA selection	Experimental Factor: genotype:abcb4 /	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP146895	Illumina NovaSeq 6000 paired end sequencing; RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month	ENA FIRST PUBLIC:2023 07 14\|ENA LAST UPDATE:2023 07 14	8680-JP-0010_S1_L005_R1_001.fastq.gz 8680-JP-0010_S1_L005_R2_001.fastq.gz	fastq fastq	21517298566.0	71249333.0	E MTAB 12901:8680 JP 0010 S1 L005 R	0:151 1:151	A:5890133399;C:4693794003;G:5193013881;T:5709021540;N:31335743	151	151			5890133399	4693794003	5193013881	5709021540	31335743	ERX10689982	ERS15395527	ERA23235100	VANDERBILT UNIVERSITY\|European Nucleotide Archive	VANDERBILT UNIVERSITY\|European Nucleotide Archive	2	0.92431	0.92248	0.13476	0.13116	0.70203	0.70283	0.50087	0.50123	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2023-07-14	Adult	Adult	Brain	Nervous System
11720	11720	ERR11282338	ERX10689981	ERS15395526	ERP146895	PRJEB61813	RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month	E-MTAB-12901	Other	The ATP binding cassette subfamily B member 1 ABCB1 encoding a multidrug transporter P glycoprotein plays a critical role in the efflux of xenobiotics in humans and is implicated in cancer resistance to chemotherapy—however little information regarding Pgp at the zebrafish. In addition to study the function of Pgp in the zebrafish brain in the aging process we performed RNA seq using brain tissue of WT and abcb4 knockout zebrafish at different ages such as 2 month and 30 month.	ENA FIRST PUBLIC:2023 07 14\|ENA LAST UPDATE:2023 07 14	Protocols: brain tissue were dissected from zebrafish and snap frozen until RNA isolation Trizol + zymo RNA clean column kit TruSeq RNA sample prep kit Illumina to prepare cDNA libraries post PolyA selection	Sample 5	SAMEA113400380	VANDERBILT UNIVERSITY	ENA FIRST PUBLIC:2023 07 14T00:23:41Z\|ENA LAST UPDATE:2023 07 14T00:23:41Z\|External Id:SAMEA113400380\|INSDC center alias:VANDERBILT UNIVERSITY\|INSDC center name:VANDERBILT UNIVERSITY\|INSDC first public:2023 07 14T00:23:41Z\|INSDC last update:2023 07 14T00:23:41Z\|INSDC status:public\|Submitter Id:E MTAB 12901:Sample 5\|age:30\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|disease:normal\|genotype:abcb4 / \|organism part:brain\|sample name:E MTAB 12901:Sample 5\|scientific name:Danio rerio\|sex:female\|strain:AB	Illumina NovaSeq 6000 paired end sequencing; RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month	E MTAB 12901:Sample 5 p	Sample 5 p	RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month	brain tissue were dissected from zebrafish and snap frozen until RNA isolation Trizol + zymo RNA clean column kit TruSeq RNA sample prep kit Illumina to prepare cDNA libraries post PolyA selection	Experimental Factor: genotype:abcb4 /	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP146895	Illumina NovaSeq 6000 paired end sequencing; RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month	ENA FIRST PUBLIC:2023 07 14\|ENA LAST UPDATE:2023 07 14	8680-JP-0005_S1_L005_R1_001.fastq.gz 8680-JP-0005_S1_L005_R2_001.fastq.gz	fastq fastq	25670665306.0	85002203.0	E MTAB 12901:8680 JP 0005 S1 L005 R	0:151 1:151	A:7004508034;C:5563021332;G:6252648683;T:6813680645;N:36806612	151	151			7004508034	5563021332	6252648683	6813680645	36806612	ERX10689981	ERS15395526	ERA23235100	VANDERBILT UNIVERSITY\|European Nucleotide Archive	VANDERBILT UNIVERSITY\|European Nucleotide Archive	2	0.92268	0.92095	0.13119	0.12796	0.70234	0.70276	0.51658	0.51519	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2023-07-14	Adult	Adult	Brain	Nervous System
11721	11721	ERR11282337	ERX10689980	ERS15395525	ERP146895	PRJEB61813	RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month	E-MTAB-12901	Other	The ATP binding cassette subfamily B member 1 ABCB1 encoding a multidrug transporter P glycoprotein plays a critical role in the efflux of xenobiotics in humans and is implicated in cancer resistance to chemotherapy—however little information regarding Pgp at the zebrafish. In addition to study the function of Pgp in the zebrafish brain in the aging process we performed RNA seq using brain tissue of WT and abcb4 knockout zebrafish at different ages such as 2 month and 30 month.	ENA FIRST PUBLIC:2023 07 14\|ENA LAST UPDATE:2023 07 14	Protocols: brain tissue were dissected from zebrafish and snap frozen until RNA isolation Trizol + zymo RNA clean column kit TruSeq RNA sample prep kit Illumina to prepare cDNA libraries post PolyA selection	Sample 4	SAMEA113400379	VANDERBILT UNIVERSITY	ENA FIRST PUBLIC:2023 07 14T00:23:41Z\|ENA LAST UPDATE:2023 07 14T00:23:41Z\|External Id:SAMEA113400379\|INSDC center alias:VANDERBILT UNIVERSITY\|INSDC center name:VANDERBILT UNIVERSITY\|INSDC first public:2023 07 14T00:23:41Z\|INSDC last update:2023 07 14T00:23:41Z\|INSDC status:public\|Submitter Id:E MTAB 12901:Sample 4\|age:30\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|disease:normal\|genotype:abcb4 / \|organism part:brain\|sample name:E MTAB 12901:Sample 4\|scientific name:Danio rerio\|sex:female\|strain:AB	Illumina NovaSeq 6000 paired end sequencing; RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month	E MTAB 12901:Sample 4 p	Sample 4 p	RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month	brain tissue were dissected from zebrafish and snap frozen until RNA isolation Trizol + zymo RNA clean column kit TruSeq RNA sample prep kit Illumina to prepare cDNA libraries post PolyA selection	Experimental Factor: genotype:abcb4 /	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP146895	Illumina NovaSeq 6000 paired end sequencing; RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month	ENA FIRST PUBLIC:2023 07 14\|ENA LAST UPDATE:2023 07 14	8680-JP-0004_S1_L005_R1_001.fastq.gz 8680-JP-0004_S1_L005_R2_001.fastq.gz	fastq fastq	19678467074.0	65160487.0	E MTAB 12901:8680 JP 0004 S1 L005 R	0:151 1:151	A:5388172969;C:4290008191;G:4741082570;T:5230699181;N:28504163	151	151			5388172969	4290008191	4741082570	5230699181	28504163	ERX10689980	ERS15395525	ERA23235100	VANDERBILT UNIVERSITY\|European Nucleotide Archive	VANDERBILT UNIVERSITY\|European Nucleotide Archive	2	0.92019	0.91807	0.13779	0.13325	0.69739	0.69682	0.48956	0.48353	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2023-07-14	Adult	Adult	Brain	Nervous System
11722	11722	ERR11282336	ERX10689979	ERS15395524	ERP146895	PRJEB61813	RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month	E-MTAB-12901	Other	The ATP binding cassette subfamily B member 1 ABCB1 encoding a multidrug transporter P glycoprotein plays a critical role in the efflux of xenobiotics in humans and is implicated in cancer resistance to chemotherapy—however little information regarding Pgp at the zebrafish. In addition to study the function of Pgp in the zebrafish brain in the aging process we performed RNA seq using brain tissue of WT and abcb4 knockout zebrafish at different ages such as 2 month and 30 month.	ENA FIRST PUBLIC:2023 07 14\|ENA LAST UPDATE:2023 07 14	Protocols: brain tissue were dissected from zebrafish and snap frozen until RNA isolation Trizol + zymo RNA clean column kit TruSeq RNA sample prep kit Illumina to prepare cDNA libraries post PolyA selection	Sample 12	SAMEA113400378	VANDERBILT UNIVERSITY	ENA FIRST PUBLIC:2023 07 14T00:23:41Z\|ENA LAST UPDATE:2023 07 14T00:23:41Z\|External Id:SAMEA113400378\|INSDC center alias:VANDERBILT UNIVERSITY\|INSDC center name:VANDERBILT UNIVERSITY\|INSDC first public:2023 07 14T00:23:41Z\|INSDC last update:2023 07 14T00:23:41Z\|INSDC status:public\|Submitter Id:E MTAB 12901:Sample 12\|age:30\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|disease:normal\|genotype:abcb4 / \|organism part:brain\|sample name:E MTAB 12901:Sample 12\|scientific name:Danio rerio\|sex:female\|strain:AB	Illumina NovaSeq 6000 paired end sequencing; RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month	E MTAB 12901:Sample 12 p	Sample 12 p	RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month	brain tissue were dissected from zebrafish and snap frozen until RNA isolation Trizol + zymo RNA clean column kit TruSeq RNA sample prep kit Illumina to prepare cDNA libraries post PolyA selection	Experimental Factor: genotype:abcb4 /	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP146895	Illumina NovaSeq 6000 paired end sequencing; RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month	ENA FIRST PUBLIC:2023 07 14\|ENA LAST UPDATE:2023 07 14	8680-JP-0012_S1_L005_R1_001.fastq.gz 8680-JP-0012_S1_L005_R2_001.fastq.gz	fastq fastq	19025354324.0	62997862.0	E MTAB 12901:8680 JP 0012 S1 L005 R	0:151 1:151	A:5203524540;C:4195830684;G:4551047863;T:5047420365;N:27530872	151	151			5203524540	4195830684	4551047863	5047420365	27530872	ERX10689979	ERS15395524	ERA23235100	VANDERBILT UNIVERSITY\|European Nucleotide Archive	VANDERBILT UNIVERSITY\|European Nucleotide Archive	2	0.92091	0.92095	0.13145	0.12737	0.69238	0.69258	0.50372	0.48431	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2023-07-14	Adult	Adult	Brain	Nervous System
11813	11813	ERR11788863	ERX11187331	ERS16221143	ERP149944	PRJEB64780	A single cell transcriptomic atlas reveals a new myeloid parenchymal population in the zebrafish brain	E-MTAB-13223	Transcriptome Analysis	To understand the cellular basis of the immune compartment of the zebrafish brain we have established reliable protocols for dissociation and prospective isolation of brain leukocytes using fluorescent transgenic lines. By combining this approach with single cell RNA sequencing we have generated a gene expression atlas composed of the distinct immune cells present in the homeostatic brain. These analyses revealed the presence of subpopulations of mononuclear phagocytes and other leukocytes including cell types that have not been or have been poorly characterized so far. Here we present the characterization of a new mononuclear phagocyte population that represents an important fraction among all brain leukocytes. Adult brain single cell suspensions were prepared from adult Tgp2ry12:GFP; cd45:DsRed fish n=3 and a total of 14 000 cd45:DsRed+ cells were processed for single cell profiling using the 10x Genomics platform.	ENA FIRST PUBLIC:2023 12 25\|ENA LAST UPDATE:2023 12 25	Protocols: FACS sorting of cd45:Dsred cells. Brains from adult Tgp2ry12:GFP; cd45:DsRed fish n=3 were dissected in 0.9X Dulbecco′s Phosphate Buffered Saline DPBS were triturated and treated with Liberase TM at 33°C for 30 45 minutes fully dissociated using a syringe with a 26G needle and washed in 2% fetal bovine serum diluted in 0.9X DPBS. Cell suspensions were centrifuged at 290g 4ºC 10 min and filtered through a 40µm nylon mesh. Just before flow cytometry analysis using calcein violet to exclude dead cells 1µM Thermo Fisher. Flow cytometry acquisition and cell sorting was performed on a FACS ARIA II Becton Dickinson. RNA Illumina	Sample 1	SAMEA114235870	Universite Libre de Bruxelles	ENA FIRST PUBLIC:2023 12 25T01:15:29Z\|ENA LAST UPDATE:2023 12 25T01:15:29Z\|External Id:SAMEA114235870\|INSDC center name:Universite Libre de Bruxelles\|INSDC first public:2023 12 25T01:15:29Z\|INSDC last update:2023 12 25T01:15:29Z\|INSDC status:public\|Submitter Id:E MTAB 13223:Sample 1\|age:5\|broker name:ArrayExpress\|cell type:leukocyte\|collection date:not collected\|common name:zebrafish\|developmental stage:adult\|genotype:wild type genotype\|geographic location country and/or sea:not collected\|individual:pool of 3 fish\|isolate:not applicable\|organism part:brain\|sample name:E MTAB 13223:Sample 1\|scientific name:Danio rerio\|sex:male and female\|strain:AB	A single cell transcriptomic atlas reveals a new myeloid parenchymal population in the zebrafish brain	E MTAB 13223:Sample 1 p	Sample 1 p	A single cell transcriptomic atlas reveals a new myeloid parenchymal population in the zebrafish brain	FACS sorting of cd45:Dsred cells. Brains from adult Tgp2ry12:GFP; cd45:DsRed fish n=3 were dissected in 0.9X Dulbecco′s Phosphate Buffered Saline DPBS were triturated and treated with Liberase TM at 33°C for 30 45 minutes fully dissociated using a syringe with a 26G needle and washed in 2% fetal bovine serum diluted in 0.9X DPBS. Cell suspensions were centrifuged at 290g 4ºC 10 min and filtered through a 40µm nylon mesh. Just before flow cytometry analysis using calcein violet to exclude dead cells 1µM Thermo Fisher. Flow cytometry acquisition and cell sorting was performed on a FACS ARIA II Becton Dickinson. RNA Illumina		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	PAIRED	ILLUMINA	NextSeq 550		ERP149944	NextSeq 550 paired end sequencing; A single cell transcriptomic atlas reveals a new myeloid parenchymal population in the zebrafish brain	ENA FIRST PUBLIC:2023 12 25\|ENA LAST UPDATE:2023 12 25	L41805_Track-81843_R1.fastq.gz L41805_Track-81843_R2.fastq.gz	fastq fastq	5545444464.0	66017196.0	E MTAB 13223:L41805 Track 81843	0:28 1:56	A:1576174024;C:1193175858;G:1221776615;T:1551009004;N:3308963	28	56			1576174024	1193175858	1221776615	1551009004	3308963	ERX11187331	ERS16221143	ERA26318932	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive	2	0.00738	0.90151	0.00285	0.20553	0.99072	0.82402	0.4645	0.53817	28	56	T	B	sc-like readlen	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_droplet	10x	United Kingdom	2023-12-25	Adult	Adult	Brain	Nervous System
11814	11814	ERR11788864	ERX11187331	ERS16221143	ERP149944	PRJEB64780	A single cell transcriptomic atlas reveals a new myeloid parenchymal population in the zebrafish brain	E-MTAB-13223	Transcriptome Analysis	To understand the cellular basis of the immune compartment of the zebrafish brain we have established reliable protocols for dissociation and prospective isolation of brain leukocytes using fluorescent transgenic lines. By combining this approach with single cell RNA sequencing we have generated a gene expression atlas composed of the distinct immune cells present in the homeostatic brain. These analyses revealed the presence of subpopulations of mononuclear phagocytes and other leukocytes including cell types that have not been or have been poorly characterized so far. Here we present the characterization of a new mononuclear phagocyte population that represents an important fraction among all brain leukocytes. Adult brain single cell suspensions were prepared from adult Tgp2ry12:GFP; cd45:DsRed fish n=3 and a total of 14 000 cd45:DsRed+ cells were processed for single cell profiling using the 10x Genomics platform.	ENA FIRST PUBLIC:2023 12 25\|ENA LAST UPDATE:2023 12 25	Protocols: FACS sorting of cd45:Dsred cells. Brains from adult Tgp2ry12:GFP; cd45:DsRed fish n=3 were dissected in 0.9X Dulbecco′s Phosphate Buffered Saline DPBS were triturated and treated with Liberase TM at 33°C for 30 45 minutes fully dissociated using a syringe with a 26G needle and washed in 2% fetal bovine serum diluted in 0.9X DPBS. Cell suspensions were centrifuged at 290g 4ºC 10 min and filtered through a 40µm nylon mesh. Just before flow cytometry analysis using calcein violet to exclude dead cells 1µM Thermo Fisher. Flow cytometry acquisition and cell sorting was performed on a FACS ARIA II Becton Dickinson. RNA Illumina	Sample 1	SAMEA114235870	Universite Libre de Bruxelles	ENA FIRST PUBLIC:2023 12 25T01:15:29Z\|ENA LAST UPDATE:2023 12 25T01:15:29Z\|External Id:SAMEA114235870\|INSDC center name:Universite Libre de Bruxelles\|INSDC first public:2023 12 25T01:15:29Z\|INSDC last update:2023 12 25T01:15:29Z\|INSDC status:public\|Submitter Id:E MTAB 13223:Sample 1\|age:5\|broker name:ArrayExpress\|cell type:leukocyte\|collection date:not collected\|common name:zebrafish\|developmental stage:adult\|genotype:wild type genotype\|geographic location country and/or sea:not collected\|individual:pool of 3 fish\|isolate:not applicable\|organism part:brain\|sample name:E MTAB 13223:Sample 1\|scientific name:Danio rerio\|sex:male and female\|strain:AB	A single cell transcriptomic atlas reveals a new myeloid parenchymal population in the zebrafish brain	E MTAB 13223:Sample 1 p	Sample 1 p	A single cell transcriptomic atlas reveals a new myeloid parenchymal population in the zebrafish brain	FACS sorting of cd45:Dsred cells. Brains from adult Tgp2ry12:GFP; cd45:DsRed fish n=3 were dissected in 0.9X Dulbecco′s Phosphate Buffered Saline DPBS were triturated and treated with Liberase TM at 33°C for 30 45 minutes fully dissociated using a syringe with a 26G needle and washed in 2% fetal bovine serum diluted in 0.9X DPBS. Cell suspensions were centrifuged at 290g 4ºC 10 min and filtered through a 40µm nylon mesh. Just before flow cytometry analysis using calcein violet to exclude dead cells 1µM Thermo Fisher. Flow cytometry acquisition and cell sorting was performed on a FACS ARIA II Becton Dickinson. RNA Illumina		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	PAIRED	ILLUMINA	NextSeq 550		ERP149944	NextSeq 550 paired end sequencing; A single cell transcriptomic atlas reveals a new myeloid parenchymal population in the zebrafish brain	ENA FIRST PUBLIC:2023 12 25\|ENA LAST UPDATE:2023 12 25	L41805_Track-81377_R1.fastq.gz L41805_Track-81377_R2.fastq.gz	fastq fastq	3184137096.0	37906394.0	E MTAB 13223:L41805 Track 81377	0:28 1:56	A:899943184;C:685571078;G:703849582;T:889228559;N:5544693	28	56			899943184	685571078	703849582	889228559	5544693	ERX11187331	ERS16221143	ERA26318932	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive	2	0.00734	0.90077	0.00293	0.20318	0.99064	0.82765	0.47994	0.53473	28	56	T	B	sc-like readlen	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_droplet	10x	United Kingdom	2023-12-25	Adult	Adult	Brain	Nervous System
26525	26525	SRR26078869	SRX21793734	SRS18895475	SRP461206	PRJNA1018104	Global liver transcriptome assay of WT Igfbp7 null mutant and Igfbp7 LOE animals	PRJNA1018104	Other	The global increased expression of Insulin like growth factor binding protein 7 IGFBP7 has been detected in non alcoholic fatty liver disease NAFLD patients however its roles in NAFLD and the mechanism remain largely unclear. The goal of this study is to investigate the effect and mechanism of Igfbp7 using a zebrafish NAFLD model. The igfbp7 / null zebrafish mutant and the Igfbp7 liver overexpressed LOE transgenic zebrafish based on Gal4/UAS system were generated by CRISPR/Cas9 and Tol2 transgenic technique respectively. The zebrafish NAFLD models in wildtypes igfbp7 / mutants and Igfbp7 LOE fishes have been established by high fat diet feeding. The Igfbp7 dynamic expression and its effects on NAFLD progression have been detected and analyzed in both human NAFLD patients and zebrafish models. And the potential mechanism has been investigated through transcriptome analysis and subsequent detection and verification.			liver specific overexpression of Igfbp7 3	LOE replicate 3		strain:transgenic strain\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:3 mpf\|dev stage:adult\|collection date:2021 10 09\|geo loc name:China:Shanxi\|sex:male\|tissue:Liver\|biomaterial provider:Zebrafish Facility of the Institute of Biomedical Sciences Shanxi University\|birth date:09 Jun 2021\|birth location:China:Shanxi\|breeding history:Fishes were fed 4 times per day with a high fat diet\|breeding method:a high fat diet in which 5% cholesterol was added to the standard diet feed type:Marvbeni C1 corresponding to 40 mg/fish/day\|replicate:LOE replicate=biological replicate3\|BioSampleModel:Model organism or animal	liver specific overexpression of Igfbp7 3	LOE3	LOE3	liver specific overexpression of Igfbp7 3			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP461206			LOE3_1.fq.gz LOE3_2.fq.gz	fastq fastq	7457209500.0	24857365.0	LOE3 1.fq.gz	0:150 1:150	A:1965670426;C:1773372970;G:1762457648;T:1955346803;N:361653	150	150			1965670426	1773372970	1762457648	1955346803	361653	SRX21793734	SRS18895475	SRA1713671	First Hospital of Shanxi Medical University\|Department of Gastroenterology and Hepatology	First Hospital of Shanxi Medical University	2	0.89541	0.89576	0.04195	0.04177	0.82536	0.82375	0.53368	0.5374	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2023-09-16	Adult	Adult	Liver	Liver and Biliary System
26526	26526	SRR26078870	SRX21793733	SRS18895474	SRP461206	PRJNA1018104	Global liver transcriptome assay of WT Igfbp7 null mutant and Igfbp7 LOE animals	PRJNA1018104	Other	The global increased expression of Insulin like growth factor binding protein 7 IGFBP7 has been detected in non alcoholic fatty liver disease NAFLD patients however its roles in NAFLD and the mechanism remain largely unclear. The goal of this study is to investigate the effect and mechanism of Igfbp7 using a zebrafish NAFLD model. The igfbp7 / null zebrafish mutant and the Igfbp7 liver overexpressed LOE transgenic zebrafish based on Gal4/UAS system were generated by CRISPR/Cas9 and Tol2 transgenic technique respectively. The zebrafish NAFLD models in wildtypes igfbp7 / mutants and Igfbp7 LOE fishes have been established by high fat diet feeding. The Igfbp7 dynamic expression and its effects on NAFLD progression have been detected and analyzed in both human NAFLD patients and zebrafish models. And the potential mechanism has been investigated through transcriptome analysis and subsequent detection and verification.			liver specific overexpression of Igfbp7 2	LOE replicate 2		strain:transgenic strain\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:3 mpf\|dev stage:adult\|collection date:2021 10 09\|geo loc name:China:Shanxi\|sex:male\|tissue:Liver\|biomaterial provider:Zebrafish Facility of the Institute of Biomedical Sciences Shanxi University\|birth date:09 Jun 2021\|birth location:China:Shanxi\|breeding history:Fishes were fed 4 times per day with a high fat diet\|breeding method:a high fat diet in which 5% cholesterol was added to the standard diet feed type:Marvbeni C1 corresponding to 40 mg/fish/day\|replicate:LOE replicate=biological replicate2\|BioSampleModel:Model organism or animal	liver specific overexpression of Igfbp7 2	LOE2	LOE2	liver specific overexpression of Igfbp7 2			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP461206			LOE2_1.fq.gz LOE2_2.fq.gz	fastq fastq	7069059900.0	23563533.0	LOE2 1.fq.gz	0:150 1:150	A:1835774064;C:1704925495;G:1698942360;T:1829075424;N:342557	150	150			1835774064	1704925495	1698942360	1829075424	342557	SRX21793733	SRS18895474	SRA1713671	First Hospital of Shanxi Medical University\|Department of Gastroenterology and Hepatology	First Hospital of Shanxi Medical University	2	0.89965	0.90019	0.0524	0.05247	0.80669	0.80525	0.53582	0.49543	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2023-09-16	Adult	Adult	Liver	Liver and Biliary System
26527	26527	SRR26078871	SRX21793732	SRS18895473	SRP461206	PRJNA1018104	Global liver transcriptome assay of WT Igfbp7 null mutant and Igfbp7 LOE animals	PRJNA1018104	Other	The global increased expression of Insulin like growth factor binding protein 7 IGFBP7 has been detected in non alcoholic fatty liver disease NAFLD patients however its roles in NAFLD and the mechanism remain largely unclear. The goal of this study is to investigate the effect and mechanism of Igfbp7 using a zebrafish NAFLD model. The igfbp7 / null zebrafish mutant and the Igfbp7 liver overexpressed LOE transgenic zebrafish based on Gal4/UAS system were generated by CRISPR/Cas9 and Tol2 transgenic technique respectively. The zebrafish NAFLD models in wildtypes igfbp7 / mutants and Igfbp7 LOE fishes have been established by high fat diet feeding. The Igfbp7 dynamic expression and its effects on NAFLD progression have been detected and analyzed in both human NAFLD patients and zebrafish models. And the potential mechanism has been investigated through transcriptome analysis and subsequent detection and verification.			liver specific overexpression of Igfbp7 1	LOE replicate 1		strain:transgenic strain\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:3 mpf\|dev stage:adult\|collection date:2021 10 09\|geo loc name:China:Shanxi\|sex:male\|tissue:Liver\|biomaterial provider:Zebrafish Facility of the Institute of Biomedical Sciences Shanxi University\|birth date:09 Jun 2021\|birth location:China:Shanxi\|breeding history:Fishes were fed 4 times per day with a high fat diet\|breeding method:a high fat diet in which 5% cholesterol was added to the standard diet feed type:Marvbeni C1 corresponding to 40 mg/fish/day\|replicate:LOE replicate=biological replicate1\|BioSampleModel:Model organism or animal	liver specific overexpression of Igfbp7 1	LOE1	LOE1	liver specific overexpression of Igfbp7 1			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP461206			LOE1_1.fq.gz LOE1_2.fq.gz	fastq fastq	7110174300.0	23700581.0	LOE1 1.fq.gz	0:150 1:150	A:1847016218;C:1713941614;G:1708466537;T:1840442742;N:307189	150	150			1847016218	1713941614	1708466537	1840442742	307189	SRX21793732	SRS18895473	SRA1713671	First Hospital of Shanxi Medical University\|Department of Gastroenterology and Hepatology	First Hospital of Shanxi Medical University	2	0.8999	0.89917	0.04883	0.04874	0.80858	0.80716	0.51686	0.52442	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2023-09-16	Adult	Adult	Liver	Liver and Biliary System
26528	26528	SRR26078872	SRX21793731	SRS18895469	SRP461206	PRJNA1018104	Global liver transcriptome assay of WT Igfbp7 null mutant and Igfbp7 LOE animals	PRJNA1018104	Other	The global increased expression of Insulin like growth factor binding protein 7 IGFBP7 has been detected in non alcoholic fatty liver disease NAFLD patients however its roles in NAFLD and the mechanism remain largely unclear. The goal of this study is to investigate the effect and mechanism of Igfbp7 using a zebrafish NAFLD model. The igfbp7 / null zebrafish mutant and the Igfbp7 liver overexpressed LOE transgenic zebrafish based on Gal4/UAS system were generated by CRISPR/Cas9 and Tol2 transgenic technique respectively. The zebrafish NAFLD models in wildtypes igfbp7 / mutants and Igfbp7 LOE fishes have been established by high fat diet feeding. The Igfbp7 dynamic expression and its effects on NAFLD progression have been detected and analyzed in both human NAFLD patients and zebrafish models. And the potential mechanism has been investigated through transcriptome analysis and subsequent detection and verification.			Igfbp7 Konckout 3	KO replicate 3		strain:mutant\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:3 mpf\|dev stage:adult\|collection date:2021 10 09\|geo loc name:China:Shanxi\|sex:male\|tissue:Liver\|biomaterial provider:Zebrafish Facility of the Institute of Biomedical Sciences Shanxi University\|birth date:09 Jun 2021\|birth location:China:Shanxi\|breeding history:Fishes were fed 4 times per day with a high fat diet\|breeding method:a high fat diet in which 5% cholesterol was added to the standard diet feed type:Marvbeni C1 corresponding to 40 mg/fish/day\|replicate:KO replicate=biological replicate3\|BioSampleModel:Model organism or animal	Igfbp7 Konckout 3	KO3	KO3	Igfbp7 Konckout 3			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP461206			KO3_1.fq.gz KO3_2.fq.gz	fastq fastq	6966225300.0	23220751.0	KO3 1.fq.gz	0:150 1:150	A:1854162705;C:1635332068;G:1634647432;T:1841746656;N:336439	150	150			1854162705	1635332068	1634647432	1841746656	336439	SRX21793731	SRS18895469	SRA1713671	First Hospital of Shanxi Medical University\|Department of Gastroenterology and Hepatology	First Hospital of Shanxi Medical University	2	0.94279	0.94294	0.0551	0.05481	0.78861	0.78739	0.54327	0.50468	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2023-09-16	Adult	Adult	Liver	Liver and Biliary System
26529	26529	SRR26078873	SRX21793730	SRS18895470	SRP461206	PRJNA1018104	Global liver transcriptome assay of WT Igfbp7 null mutant and Igfbp7 LOE animals	PRJNA1018104	Other	The global increased expression of Insulin like growth factor binding protein 7 IGFBP7 has been detected in non alcoholic fatty liver disease NAFLD patients however its roles in NAFLD and the mechanism remain largely unclear. The goal of this study is to investigate the effect and mechanism of Igfbp7 using a zebrafish NAFLD model. The igfbp7 / null zebrafish mutant and the Igfbp7 liver overexpressed LOE transgenic zebrafish based on Gal4/UAS system were generated by CRISPR/Cas9 and Tol2 transgenic technique respectively. The zebrafish NAFLD models in wildtypes igfbp7 / mutants and Igfbp7 LOE fishes have been established by high fat diet feeding. The Igfbp7 dynamic expression and its effects on NAFLD progression have been detected and analyzed in both human NAFLD patients and zebrafish models. And the potential mechanism has been investigated through transcriptome analysis and subsequent detection and verification.			Igfbp7 Konckout 2	KO replicate 2		strain:mutant\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:3 mpf\|dev stage:adult\|collection date:2021 10 09\|geo loc name:China:Shanxi\|sex:male\|tissue:Liver\|biomaterial provider:Zebrafish Facility of the Institute of Biomedical Sciences Shanxi University\|birth date:09 Jun 2021\|birth location:China:Shanxi\|breeding history:Fishes were fed 4 times per day with a high fat diet\|breeding method:a high fat diet in which 5% cholesterol was added to the standard diet feed type:Marvbeni C1 corresponding to 40 mg/fish/day\|replicate:KO replicate=biological replicate2\|BioSampleModel:Model organism or animal	Igfbp7 Konckout 2	KO2	KO2	Igfbp7 Konckout 2			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP461206			KO2_1.fq.gz KO2_2.fq.gz	fastq fastq	7465655100.0	24885517.0	KO2 1.fq.gz	0:150 1:150	A:1988715771;C:1750416778;G:1753335257;T:1972838856;N:348438	150	150			1988715771	1750416778	1753335257	1972838856	348438	SRX21793730	SRS18895470	SRA1713671	First Hospital of Shanxi Medical University\|Department of Gastroenterology and Hepatology	First Hospital of Shanxi Medical University	2	0.94231	0.94227	0.04975	0.04965	0.802	0.80018	0.50781	0.54557	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2023-09-16	Adult	Adult	Liver	Liver and Biliary System
26530	26530	SRR26078874	SRX21793729	SRS18895472	SRP461206	PRJNA1018104	Global liver transcriptome assay of WT Igfbp7 null mutant and Igfbp7 LOE animals	PRJNA1018104	Other	The global increased expression of Insulin like growth factor binding protein 7 IGFBP7 has been detected in non alcoholic fatty liver disease NAFLD patients however its roles in NAFLD and the mechanism remain largely unclear. The goal of this study is to investigate the effect and mechanism of Igfbp7 using a zebrafish NAFLD model. The igfbp7 / null zebrafish mutant and the Igfbp7 liver overexpressed LOE transgenic zebrafish based on Gal4/UAS system were generated by CRISPR/Cas9 and Tol2 transgenic technique respectively. The zebrafish NAFLD models in wildtypes igfbp7 / mutants and Igfbp7 LOE fishes have been established by high fat diet feeding. The Igfbp7 dynamic expression and its effects on NAFLD progression have been detected and analyzed in both human NAFLD patients and zebrafish models. And the potential mechanism has been investigated through transcriptome analysis and subsequent detection and verification.			Igfbp7 Konckout 1	KO replicate 1		strain:mutant\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:3 mpf\|dev stage:adult\|collection date:2021 10 09\|geo loc name:China:Shanxi\|sex:male\|tissue:Liver\|biomaterial provider:Zebrafish Facility of the Institute of Biomedical Sciences Shanxi University\|birth date:09 Jun 2021\|birth location:China:Shanxi\|breeding history:Fishes were fed 4 times per day with a high fat diet\|breeding method:a high fat diet in which 5% cholesterol was added to the standard diet feed type:Marvbeni C1 corresponding to 40 mg/fish/day\|replicate:KO replicate=biological replicate1\|BioSampleModel:Model organism or animal	Igfbp7 Konckout 1	KO1	KO1	Igfbp7 Konckout 1			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP461206			KO1_1.fq.gz KO1_2.fq.gz	fastq fastq	7208655000.0	24028850.0	KO1 1.fq.gz	0:150 1:150	A:1937720737;C:1672178897;G:1677582029;T:1920894866;N:278471	150	150			1937720737	1672178897	1677582029	1920894866	278471	SRX21793729	SRS18895472	SRA1713671	First Hospital of Shanxi Medical University\|Department of Gastroenterology and Hepatology	First Hospital of Shanxi Medical University	2	0.93429	0.93361	0.05126	0.05122	0.80827	0.80718	0.48739	0.49469	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2023-09-16	Adult	Adult	Liver	Liver and Biliary System
26531	26531	SRR26078875	SRX21793728	SRS18895471	SRP461206	PRJNA1018104	Global liver transcriptome assay of WT Igfbp7 null mutant and Igfbp7 LOE animals	PRJNA1018104	Other	The global increased expression of Insulin like growth factor binding protein 7 IGFBP7 has been detected in non alcoholic fatty liver disease NAFLD patients however its roles in NAFLD and the mechanism remain largely unclear. The goal of this study is to investigate the effect and mechanism of Igfbp7 using a zebrafish NAFLD model. The igfbp7 / null zebrafish mutant and the Igfbp7 liver overexpressed LOE transgenic zebrafish based on Gal4/UAS system were generated by CRISPR/Cas9 and Tol2 transgenic technique respectively. The zebrafish NAFLD models in wildtypes igfbp7 / mutants and Igfbp7 LOE fishes have been established by high fat diet feeding. The Igfbp7 dynamic expression and its effects on NAFLD progression have been detected and analyzed in both human NAFLD patients and zebrafish models. And the potential mechanism has been investigated through transcriptome analysis and subsequent detection and verification.			wild type 3	WT replicate 3		strain:wild type\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:3 mpf\|dev stage:adult\|collection date:2021 10 09\|geo loc name:China:Shanxi\|sex:male\|tissue:Liver\|biomaterial provider:Zebrafish Facility of the Institute of Biomedical Sciences Shanxi University\|birth date:09 Jun 2021\|birth location:China:Shanxi\|breeding history:Fishes were fed 4 times per day with a high fat diet\|breeding method:a high fat diet in which 5% cholesterol was added to the standard diet feed type:Marvbeni C1 corresponding to 40 mg/fish/day\|replicate:WT replicate=biological replicate3\|BioSampleModel:Model organism or animal	wild type 3	WT3	WT3	wild type 3			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP461206			WT3_1.fq.gz WT3_2.fq.gz	fastq fastq	7267116600.0	24223722.0	WT3 1.fq.gz	0:150 1:150	A:1946606247;C:1693037772;G:1694230444;T:1932894815;N:347322	150	150			1946606247	1693037772	1694230444	1932894815	347322	SRX21793728	SRS18895471	SRA1713671	First Hospital of Shanxi Medical University\|Department of Gastroenterology and Hepatology	First Hospital of Shanxi Medical University	2	0.94026	0.94007	0.05203	0.05132	0.79622	0.79393	0.52332	0.51051	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2023-09-16	Adult	Adult	Liver	Liver and Biliary System
26532	26532	SRR26078876	SRX21793727	SRS18895467	SRP461206	PRJNA1018104	Global liver transcriptome assay of WT Igfbp7 null mutant and Igfbp7 LOE animals	PRJNA1018104	Other	The global increased expression of Insulin like growth factor binding protein 7 IGFBP7 has been detected in non alcoholic fatty liver disease NAFLD patients however its roles in NAFLD and the mechanism remain largely unclear. The goal of this study is to investigate the effect and mechanism of Igfbp7 using a zebrafish NAFLD model. The igfbp7 / null zebrafish mutant and the Igfbp7 liver overexpressed LOE transgenic zebrafish based on Gal4/UAS system were generated by CRISPR/Cas9 and Tol2 transgenic technique respectively. The zebrafish NAFLD models in wildtypes igfbp7 / mutants and Igfbp7 LOE fishes have been established by high fat diet feeding. The Igfbp7 dynamic expression and its effects on NAFLD progression have been detected and analyzed in both human NAFLD patients and zebrafish models. And the potential mechanism has been investigated through transcriptome analysis and subsequent detection and verification.			wild type 2	WT replicate 2		strain:wild type\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:3 mpf\|dev stage:adult\|collection date:2021 10 09\|geo loc name:China:Shanxi\|sex:male\|tissue:Liver\|biomaterial provider:Zebrafish Facility of the Institute of Biomedical Sciences Shanxi University\|birth date:09 Jun 2021\|birth location:China:Shanxi\|breeding history:Fishes were fed 4 times per day with a high fat diet\|breeding method:a high fat diet in which 5% cholesterol was added to the standard diet feed type:Marvbeni C1 corresponding to 40 mg/fish/day\|replicate:WT replicate=biological replicate2\|BioSampleModel:Model organism or animal	wild type 2	WT2	WT2	wild type 2			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP461206			WT2_1.fq.gz WT2_2.fq.gz	fastq fastq	7206849900.0	24022833.0	WT2 1.fq.gz	0:150 1:150	A:1947268148;C:1660088486;G:1665583448;T:1933561073;N:348745	150	150			1947268148	1660088486	1665583448	1933561073	348745	SRX21793727	SRS18895467	SRA1713671	First Hospital of Shanxi Medical University\|Department of Gastroenterology and Hepatology	First Hospital of Shanxi Medical University	2	0.93368	0.93327	0.06754	0.06713	0.78681	0.7861	0.53133	0.53795	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2023-09-16	Adult	Adult	Liver	Liver and Biliary System
26533	26533	SRR26078877	SRX21793726	SRS18895468	SRP461206	PRJNA1018104	Global liver transcriptome assay of WT Igfbp7 null mutant and Igfbp7 LOE animals	PRJNA1018104	Other	The global increased expression of Insulin like growth factor binding protein 7 IGFBP7 has been detected in non alcoholic fatty liver disease NAFLD patients however its roles in NAFLD and the mechanism remain largely unclear. The goal of this study is to investigate the effect and mechanism of Igfbp7 using a zebrafish NAFLD model. The igfbp7 / null zebrafish mutant and the Igfbp7 liver overexpressed LOE transgenic zebrafish based on Gal4/UAS system were generated by CRISPR/Cas9 and Tol2 transgenic technique respectively. The zebrafish NAFLD models in wildtypes igfbp7 / mutants and Igfbp7 LOE fishes have been established by high fat diet feeding. The Igfbp7 dynamic expression and its effects on NAFLD progression have been detected and analyzed in both human NAFLD patients and zebrafish models. And the potential mechanism has been investigated through transcriptome analysis and subsequent detection and verification.			wild type 1	WT replicate 1		strain:wild type\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:3 mpf\|dev stage:adult\|collection date:2021 10 09\|geo loc name:China:Shanxi\|sex:male\|tissue:Liver\|biomaterial provider:Zebrafish Facility of the Institute of Biomedical Sciences Shanxi University\|birth date:09 Jun 2021\|birth location:China:Shanxi\|breeding history:Fishes were fed 4 times per day with a high fat diet\|breeding method:a high fat diet in which 5% cholesterol was added to the standard diet feed type:Marvbeni C1 corresponding to 40 mg/fish/day\|replicate:WT replicate=biological replicate1\|BioSampleModel:Model organism or animal	wild type 1	WT1	WT1	wild type 1			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP461206			WT1_1.fq.gz WT1_2.fq.gz	fastq fastq	7170532200.0	23901774.0	WT1 1.fq.gz	0:150 1:150	A:1931584106;C:1658793663;G:1662799956;T:1917012316;N:342159	150	150			1931584106	1658793663	1662799956	1917012316	342159	SRX21793726	SRS18895468	SRA1713671	First Hospital of Shanxi Medical University\|Department of Gastroenterology and Hepatology	First Hospital of Shanxi Medical University	2	0.93456	0.93372	0.06482	0.06467	0.77327	0.77266	0.52308	0.53023	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2023-09-16	Adult	Adult	Liver	Liver and Biliary System
28882	28882	SRR26783947	SRX22482174	SRS19495555	SRP471222	PRJNA1038711	Zebrafish leukemia sequencing	PRJNA1038711	Other	Validation of an ETV6::RUNX1 positive pB ALL zebrafish model				Non leukemic kidney marrow control #2		isolate:UAS::GFP control #2\|age:9 month 16 month\|collection date:2023 01 12\|geo loc name:Finland: Tampere Europe\|sex:female\|tissue:Kidney marrow\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: non leukemic whole kidney marrow #2	A10	A10	PCR			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina HiSeq X		SRP471222			A10_EKRN230034972-1A_HHG75DSX7_L2_2.fq.gz A10_EKRN230034972-1A_HHG75DSX7_L2_1.fq.gz	fastq fastq	7982890500.0	26609635.0	A10 EKRN230034972 1A HHG75DSX7 L2 1.fq.gz	0:150 1:150	A:2129699297;C:1884782648;G:1870728993;T:2097648646;N:30916	150	150			2129699297	1884782648	1870728993	2097648646	30916	SRX22482174	SRS19495555	SRA1748743	Tampere University\|Clinical Medicine	Tampere University	2	0.93382	0.93397	0.06505	0.06535	0.69826	0.69875	0.51693	0.51829	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Finland	2023-11-10	Adult	Adult	Multi-tissue	Multi-system
28883	28883	SRR26783948	SRX22482173	SRS19495553	SRP471222	PRJNA1038711	Zebrafish leukemia sequencing	PRJNA1038711	Other	Validation of an ETV6::RUNX1 positive pB ALL zebrafish model				Non leukemic kidney marrow control #1		isolate:UAS::GFP control #1\|age:9 month 16 month\|collection date:2023 01 11\|geo loc name:Finland: Tampere Europe\|sex:male\|tissue:Kidney marrow\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: non leukemic whole kidney marrow #1	A9	A9	PCR			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina HiSeq X		SRP471222			A9_EKRN230034971-1A_HHG75DSX7_L2_1.fq.gz A9_EKRN230034971-1A_HHG75DSX7_L2_2.fq.gz	fastq fastq	6119764500.0	20399215.0	A9 EKRN230034971 1A HHG75DSX7 L2 1.fq.gz	0:150 1:150	A:1652919782;C:1426521039;G:1415190390;T:1625109104;N:24185	150	150			1652919782	1426521039	1415190390	1625109104	24185	SRX22482173	SRS19495553	SRA1748743	Tampere University\|Clinical Medicine	Tampere University	2	0.93503	0.93495	0.07197	0.07148	0.71995	0.71973	0.5119	0.51499	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Finland	2023-11-10	Adult	Adult	Multi-tissue	Multi-system
28884	28884	SRR26783949	SRX22482172	SRS19495554	SRP471222	PRJNA1038711	Zebrafish leukemia sequencing	PRJNA1038711	Other	Validation of an ETV6::RUNX1 positive pB ALL zebrafish model				ETV6::RUNX1 tumor #8		isolate:ETV6::RUNX1 knock in zebrafish #8\|age:9 month 16 month\|collection date:2023 05 10\|geo loc name:Finland: Tampere Europe\|sex:male\|tissue:Kidney marrow\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: leukemic whole kidney marrow #8	A8	A8	PCR			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina HiSeq X		SRP471222			A8_EKRN230034970-1A_HHG75DSX7_L2_1.fq.gz A8_EKRN230034970-1A_HHG75DSX7_L2_2.fq.gz	fastq fastq	7920658200.0	26402194.0	A8 EKRN230034970 1A HHG75DSX7 L2 1.fq.gz	0:150 1:150	A:2084803636;C:1894755310;G:1880741705;T:2060327167;N:30382	150	150			2084803636	1894755310	1880741705	2060327167	30382	SRX22482172	SRS19495554	SRA1748743	Tampere University\|Clinical Medicine	Tampere University	2	0.93929	0.94055	0.10937	0.1102	0.71741	0.71756	0.46004	0.46358	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Finland	2023-11-10	Adult	Adult	Multi-tissue	Multi-system
28885	28885	SRR26783950	SRX22482171	SRS19495552	SRP471222	PRJNA1038711	Zebrafish leukemia sequencing	PRJNA1038711	Other	Validation of an ETV6::RUNX1 positive pB ALL zebrafish model				ETV6::RUNX1 tumor #7		isolate:ETV6::RUNX1 knock in zebrafish #7\|age:9 month 16 month\|collection date:2023 03 09\|geo loc name:Finland: Tampere Europe\|sex:female\|tissue:Kidney marrow\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: leukemic whole kidney marrow #7	A7	A7	PCR			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina HiSeq X		SRP471222			A7_EKRN230034969-1A_HHG75DSX7_L2_2.fq.gz A7_EKRN230034969-1A_HHG75DSX7_L2_1.fq.gz	fastq fastq	8875539300.0	29585131.0	A7 EKRN230034969 1A HHG75DSX7 L2 1.fq.gz	0:150 1:150	A:2426453238;C:2049446891;G:2017593291;T:2382011570;N:34310	150	150			2426453238	2049446891	2017593291	2382011570	34310	SRX22482171	SRS19495552	SRA1748743	Tampere University\|Clinical Medicine	Tampere University	2	0.92101	0.92052	0.12337	0.12369	0.74052	0.74012	0.47692	0.47624	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Finland	2023-11-10	Adult	Adult	Multi-tissue	Multi-system
28886	28886	SRR26783951	SRX22482170	SRS19495551	SRP471222	PRJNA1038711	Zebrafish leukemia sequencing	PRJNA1038711	Other	Validation of an ETV6::RUNX1 positive pB ALL zebrafish model				ETV6::RUNX1 tumor #6		isolate:ETV6::RUNX1 knock in zebrafish #6\|age:9 month 16 month\|collection date:2023 03 08\|geo loc name:Finland: Tampere Europe\|sex:female\|tissue:Kidney marrow\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: leukemic whole kidney marrow #6	A6	A6	PCR			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina HiSeq X		SRP471222			A6_EKRN230034968-1A_HHG75DSX7_L2_1.fq.gz A6_EKRN230034968-1A_HHG75DSX7_L2_2.fq.gz	fastq fastq	7560052500.0	25200175.0	A6 EKRN230034968 1A HHG75DSX7 L2 1.fq.gz	0:150 1:150	A:2044845958;C:1762698184;G:1744547769;T:2007930943;N:29646	150	150			2044845958	1762698184	1744547769	2007930943	29646	SRX22482170	SRS19495551	SRA1748743	Tampere University\|Clinical Medicine	Tampere University	2	0.92673	0.92704	0.11586	0.1157	0.73464	0.73454	0.49457	0.49107	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Finland	2023-11-10	Adult	Adult	Multi-tissue	Multi-system
28887	28887	SRR26783952	SRX22482169	SRS19495550	SRP471222	PRJNA1038711	Zebrafish leukemia sequencing	PRJNA1038711	Other	Validation of an ETV6::RUNX1 positive pB ALL zebrafish model				ETV6::RUNX1 tumor #5		isolate:ETV6::RUNX1 knock in zebrafish #5\|age:9 month 16 month\|collection date:2023 03 07\|geo loc name:Finland: Tampere Europe\|sex:female\|tissue:Kidney marrow\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: leukemic whole kidney marrow #5	A5	A5	PCR			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina HiSeq X		SRP471222			A5_EKRN230034967-1A_HHG75DSX7_L2_1.fq.gz A5_EKRN230034967-1A_HHG75DSX7_L2_2.fq.gz	fastq fastq	8269320000.0	27564400.0	A5 EKRN230034967 1A HHG75DSX7 L2 1.fq.gz	0:150 1:150	A:2208684304;C:1954270073;G:1933348989;T:2172985012;N:31622	150	150			2208684304	1954270073	1933348989	2172985012	31622	SRX22482169	SRS19495550	SRA1748743	Tampere University\|Clinical Medicine	Tampere University	2	0.94285	0.9422	0.08987	0.08977	0.75507	0.7541	0.52032	0.50956	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Finland	2023-11-10	Adult	Adult	Multi-tissue	Multi-system
28888	28888	SRR26783953	SRX22482168	SRS19495549	SRP471222	PRJNA1038711	Zebrafish leukemia sequencing	PRJNA1038711	Other	Validation of an ETV6::RUNX1 positive pB ALL zebrafish model				ETV6::RUNX1 tumor #4		isolate:ETV6::RUNX1 knock in zebrafish #4\|age:9 month 16 month\|collection date:2023 02 06\|geo loc name:Finland: Tampere Europe\|sex:female\|tissue:Kidney marrow\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: leukemic whole kidney marrow #4	A4	A4	PCR			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina HiSeq X		SRP471222			A4_EKRN230034966-1A_HHG75DSX7_L2_2.fq.gz A4_EKRN230034966-1A_HHG75DSX7_L2_1.fq.gz	fastq fastq	6514998000.0	21716660.0	A4 EKRN230034966 1A HHG75DSX7 L2 1.fq.gz	0:150 1:150	A:1755226695;C:1525196740;G:1509297214;T:1725251790;N:25561	150	150			1755226695	1525196740	1509297214	1725251790	25561	SRX22482168	SRS19495549	SRA1748743	Tampere University\|Clinical Medicine	Tampere University	2	0.93241	0.93171	0.08147	0.08039	0.72318	0.72271	0.48554	0.48715	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Finland	2023-11-10	Adult	Adult	Multi-tissue	Multi-system
28889	28889	SRR26783954	SRX22482167	SRS19495548	SRP471222	PRJNA1038711	Zebrafish leukemia sequencing	PRJNA1038711	Other	Validation of an ETV6::RUNX1 positive pB ALL zebrafish model				ETV6::RUNX1 tumor #3		isolate:ETV6::RUNX1 knock in zebrafish #3\|age:9 month 16 month\|collection date:2023 02 05\|geo loc name:Finland: Tampere Europe\|sex:female\|tissue:Kidney marrow\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: leukemic whole kidney marrow #3	A3	A3	PCR			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina HiSeq X		SRP471222			A3_EKRN230034965-1A_HHG75DSX7_L2_1.fq.gz A3_EKRN230034965-1A_HHG75DSX7_L2_2.fq.gz	fastq fastq	7439426700.0	24798089.0	A3 EKRN230034965 1A HHG75DSX7 L2 1.fq.gz	0:150 1:150	A:1997063524;C:1750471227;G:1730255985;T:1961607399;N:28565	150	150			1997063524	1750471227	1730255985	1961607399	28565	SRX22482167	SRS19495548	SRA1748743	Tampere University\|Clinical Medicine	Tampere University	2	0.93247	0.93234	0.10911	0.10805	0.73359	0.73377	0.49804	0.4981	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Finland	2023-11-10	Adult	Adult	Multi-tissue	Multi-system
28890	28890	SRR26783955	SRX22482166	SRS19495547	SRP471222	PRJNA1038711	Zebrafish leukemia sequencing	PRJNA1038711	Other	Validation of an ETV6::RUNX1 positive pB ALL zebrafish model				Non leukemic kidney marrow control #3		isolate:UAS::GFP control #3\|age:9 month 16 month\|collection date:2023 01 13\|geo loc name:Finland: Tampere Europe\|sex:female\|tissue:Kidney marrow\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: non leukemic whole kidney marrow #3	A11	A11	PCR			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina HiSeq X		SRP471222			A11_EKRN230034973-1A_HHG75DSX7_L2_1.fq.gz A11_EKRN230034973-1A_HHG75DSX7_L2_2.fq.gz	fastq fastq	7535572200.0	25118574.0	A11 EKRN230034973 1A HHG75DSX7 L2 1.fq.gz	0:150 1:150	A:2030032446;C:1757927547;G:1745325371;T:2002258226;N:28610	150	150			2030032446	1757927547	1745325371	2002258226	28610	SRX22482166	SRS19495547	SRA1748743	Tampere University\|Clinical Medicine	Tampere University	2	0.93698	0.93781	0.07017	0.0697	0.72324	0.72316	0.52767	0.52695	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Finland	2023-11-10	Adult	Adult	Multi-tissue	Multi-system
28891	28891	SRR26783956	SRX22482165	SRS19495546	SRP471222	PRJNA1038711	Zebrafish leukemia sequencing	PRJNA1038711	Other	Validation of an ETV6::RUNX1 positive pB ALL zebrafish model				ETV6::RUNX1 tumor #2		isolate:ETV6::RUNX1 knock in zebrafish #2\|age:9 month 16 month\|collection date:2023 01 04\|geo loc name:Finland: Tampere Europe\|sex:female\|tissue:Kidney marrow\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: leukemic whole kidney marrow #2	A2	A2	PCR			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina HiSeq X		SRP471222			A2_EKRN230034964-1A_HHG75DSX7_L2_1.fq.gz A2_EKRN230034964-1A_HHG75DSX7_L2_2.fq.gz	fastq fastq	8139110700.0	27130369.0	A2 EKRN230034964 1A HHG75DSX7 L2 1.fq.gz	0:150 1:150	A:2200986080;C:1900110630;G:1876627982;T:2161354090;N:31918	150	150			2200986080	1900110630	1876627982	2161354090	31918	SRX22482165	SRS19495546	SRA1748743	Tampere University\|Clinical Medicine	Tampere University	2	0.93418	0.93374	0.11817	0.11792	0.73227	0.73251	0.49375	0.49338	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Finland	2023-11-10	Adult	Adult	Multi-tissue	Multi-system
28892	28892	SRR26783957	SRX22482164	SRS19495545	SRP471222	PRJNA1038711	Zebrafish leukemia sequencing	PRJNA1038711	Other	Validation of an ETV6::RUNX1 positive pB ALL zebrafish model				ETV6::RUNX1 tumor #1		isolate:ETV6::RUNX1 knock in zebrafish #1\|age:9 month 16 month\|collection date:2023 01 03\|geo loc name:Finland: Tampere Europe\|sex:female\|tissue:Kidney marrow\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: leukemic whole kidney marrow #1	A1	A1	PCR			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina HiSeq X		SRP471222			A1_EKRN230034963-1A_HHG75DSX7_L2_1.fq.gz A1_EKRN230034963-1A_HHG75DSX7_L2_2.fq.gz	fastq fastq	10375495200.0	34584984.0	A1 EKRN230034963 1A HHG75DSX7 L2 1.fq.gz	0:150 1:150	A:2781268558;C:2442675432;G:2417292722;T:2734218470;N:40018	150	150			2781268558	2442675432	2417292722	2734218470	40018	SRX22482164	SRS19495545	SRA1748743	Tampere University\|Clinical Medicine	Tampere University	2	0.93836	0.93801	0.12376	0.12224	0.74416	0.74406	0.49065	0.48915	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Finland	2023-11-10	Adult	Adult	Multi-tissue	Multi-system
29575	29575	SRR27387418	SRX23063709	SRS20023731	SRP480720	PRJNA1059246	Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish	PRJNA1059246	Other	Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves TWPs contain many harmful chemicals including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.			Combined Intestine	combined intestine 6		strain:Wild type\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:laboratory\|age:16 weeks\|dev stage:adult\|sex:male\|tissue:intestine\|biomaterial provider:not applicable\|birth date:not applicable\|birth location:not applicable\|breeding history:not applicable\|breeding method:not applicable\|cell line:not applicable\|cell subtype:not applicable\|cell type:not applicable\|collected by:Shubham Varshney\|collection date:2023 06\|culture collection:not applicable\|death date:not applicable\|disease:not applicable\|disease stg:not applicable\|genotype:not applicable\|geo loc name:not applicable\|growth protocol:not applicable\|health state:not applicable\|isolation source:not applicable\|lat lon:not applicable\|phenotype:not applicable\|sample type:not applicable\|specimen voucher:not applicable\|store cond:not applicable\|stud book number:not applicable\|treatment:combined intestine replicate6\|BioSampleModel:Model organism or animal	RNA Seq of zebrafish	T8 6	T8 6	PCR enrichment of adaptor ligated DNA			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	NextSeq 550		SRP480720			A54_1.fastq.gz A54_2.fastq.gz	fastq fastq	8459790000.0	28199300.0	A54 1.fastq.gz	0:150 1:150	A:2287135948;C:1957145280;G:1959338891;T:2256075943;N:93938	150	150			2287135948	1957145280	1959338891	2256075943	93938	SRX23063709	SRS20023731	SRA1777576	Nord University\|Faculty of Biosciences and Aquaculture	Nord University	2	0.92583	0.92422	0.06345	0.06263	0.75718	0.75757	0.52145	0.5361	150	150	B	B	biological fallback assumption	illumina	nextseq	unknown	poly_a	unknown	bulk	unknown	unknown	Norway	2023-12-30	Adult	Adult	Gut	Digestive System
29576	29576	SRR27387419	SRX23063708	SRS20023730	SRP480720	PRJNA1059246	Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish	PRJNA1059246	Other	Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves TWPs contain many harmful chemicals including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.			Combined Intestine	combined intestine 5		strain:Wild type\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:laboratory\|age:16 weeks\|dev stage:adult\|sex:male\|tissue:intestine\|biomaterial provider:not applicable\|birth date:not applicable\|birth location:not applicable\|breeding history:not applicable\|breeding method:not applicable\|cell line:not applicable\|cell subtype:not applicable\|cell type:not applicable\|collected by:Shubham Varshney\|collection date:2023 06\|culture collection:not applicable\|death date:not applicable\|disease:not applicable\|disease stg:not applicable\|genotype:not applicable\|geo loc name:not applicable\|growth protocol:not applicable\|health state:not applicable\|isolation source:not applicable\|lat lon:not applicable\|phenotype:not applicable\|sample type:not applicable\|specimen voucher:not applicable\|store cond:not applicable\|stud book number:not applicable\|treatment:combined intestine replicate5\|BioSampleModel:Model organism or animal	RNA Seq of zebrafish	T8 5	T8 5	PCR enrichment of adaptor ligated DNA			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	NextSeq 550		SRP480720			A53_1.fastq.gz A53_2.fastq.gz	fastq fastq	8302022700.0	27673409.0	A53 1.fastq.gz	0:150 1:150	A:2241277601;C:1925048164;G:1920142999;T:2215462687;N:91249	150	150			2241277601	1925048164	1920142999	2215462687	91249	SRX23063708	SRS20023730	SRA1777576	Nord University\|Faculty of Biosciences and Aquaculture	Nord University	2	0.92711	0.92566	0.06314	0.06353	0.75221	0.75219	0.541	0.53579	150	150	B	B	biological fallback assumption	illumina	nextseq	unknown	poly_a	unknown	bulk	unknown	unknown	Norway	2023-12-30	Adult	Adult	Gut	Digestive System
29577	29577	SRR27387420	SRX23063707	SRS20023729	SRP480720	PRJNA1059246	Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish	PRJNA1059246	Other	Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves TWPs contain many harmful chemicals including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.			Combined Intestine	combined intestine 4		strain:Wild type\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:laboratory\|age:16 weeks\|dev stage:adult\|sex:male\|tissue:intestine\|biomaterial provider:not applicable\|birth date:not applicable\|birth location:not applicable\|breeding history:not applicable\|breeding method:not applicable\|cell line:not applicable\|cell subtype:not applicable\|cell type:not applicable\|collected by:Shubham Varshney\|collection date:2023 06\|culture collection:not applicable\|death date:not applicable\|disease:not applicable\|disease stg:not applicable\|genotype:not applicable\|geo loc name:not applicable\|growth protocol:not applicable\|health state:not applicable\|isolation source:not applicable\|lat lon:not applicable\|phenotype:not applicable\|sample type:not applicable\|specimen voucher:not applicable\|store cond:not applicable\|stud book number:not applicable\|treatment:combined intestine replicate4\|BioSampleModel:Model organism or animal	RNA Seq of zebrafish	T8 4	T8 4	PCR enrichment of adaptor ligated DNA			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	NextSeq 550		SRP480720			A49_1.fastq.gz A49_2.fastq.gz	fastq fastq	6939976800.0	23133256.0	A49 1.fastq.gz	0:150 1:150	A:1895013575;C:1589528661;G:1585890890;T:1869466351;N:77323	150	150			1895013575	1589528661	1585890890	1869466351	77323	SRX23063707	SRS20023729	SRA1777576	Nord University\|Faculty of Biosciences and Aquaculture	Nord University	2	0.92632	0.92542	0.06323	0.06265	0.75588	0.75722	0.55002	0.55324	150	150	B	B	biological fallback assumption	illumina	nextseq	unknown	poly_a	unknown	bulk	unknown	unknown	Norway	2023-12-30	Adult	Adult	Gut	Digestive System

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;